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Information on EC 6.3.2.9 - UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase and Organism(s) Escherichia coli and UniProt Accession P14900
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6.3.2.9 UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligaseIUBMB Comments
Involved in the synthesis of a cell-wall peptide in bacteria.
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
murd ligase, d-glutamic acid-adding enzyme, udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase, udp-n-acetylmuramoyl-l-alanyl-d-glutamate synthetase, udp-n-acetylmuramoyl-l-alanine-d-glutamate ligase, d-glutamate-adding enzyme, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D-Glutamate-adding enzyme
-
-
-
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D-glutamic acid adding enzyme
-
-
-
-
D-Glutamic acid-adding enzyme
-
-
-
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Synthetase, uridine diphospho-N-acetylmuramoylalanyl-D-glutamate
-
-
-
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UDP-Mur-Nac-L-Ala:L-Glu ligase
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-
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UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
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-
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UDPMurNAc-L-alanine:D-glutamate ligase (ADP-forming)
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Uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase
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Uridine diphospho-N-acetylmuramoylalanyl-D-glutamate synthetase
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-
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UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
reaction via tetrahedral intermediate. The enzyme performs binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. Reaction mechanism and structure analysis, overview
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
a tetrahedral transition state follows the acyl phosphate in the reaction pathway
-
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
the catalytic mechanism involves a tetrahedral intermediate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylic acid amide formation
-
-
-
-
carboxamide formation
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-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -
SYSTEMATIC NAME
IUBMB Comments
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (ADP-forming)
Involved in the synthesis of a cell-wall peptide in bacteria.
CAS REGISTRY NUMBER
COMMENTARY
9023-59-0
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
-
-
-
?
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
key role in peptidoglycan biosynthesis
-
-
?
ATP + 1-phospho-N-acetylmuramoyl-L-Ala + Glu
ADP + phosphate + 1-phospho-N-acetylmuramoyl-L-Ala-D-Glu
-
-
-
-
?
ATP + dihydrouridine 5'-diphosphate-N-acetylmuramoyl-L-Ala + Glu
ADP + phosphate + dihydrouridine 5'-diphosphate-N-acetylmuramoyl-L-Ala-D-Glu
-
-
-
-
?
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
-
ATP in form of MgATP2-
-
-
?
ATP + UDP-N-acetylmuramate-L-alanine
adenosine 5'-tetraphosphate
-
-
-
?
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
ATP + UDP-N-acetylmuramoyl-L-Ala + (+/-)trans-1-amino-3-carboxy-cyclohexanecarboxylic acid
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-(+/-)trans-1-amino-3-carboxy-cyclohexanecarboxylic acid
-
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + (+/-)trans-1-amino-3-carboxy-cyclopentanecarboxylic acid
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-(+/-)trans-1-amino-3-carboxy-cyclopentanecarboxylic acid
-
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + D-erythro-3-methylglutamic acid
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-D-erythro-3-methylglutamic acid
-
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + D-erythro-4-methylglutamic acid
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-D-erythro-4-methylglutamic acid
-
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + DL-homocysteic acid
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-DL-homocysteic acid
-
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-D-Glu
-
-
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-D-Glu
-
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
ADP + phosphate + UDP-N-acetylmuramoyl-L-Ala-D-Glu
highly stereospecific for D-Glu
-
-
?
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
-
-
-
?
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
-
-
r
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
-
key role in peptidoglycan biosynthesis
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
-
activity is not in excess in the cell under normal growth conditions, but its amount is adjusted to the requirements of peptidoglycan synthesis
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
-
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
MurD is essential for cytoplasmic bacterial cell wall biosynthesis
-
-
?
additional information
?
-
enzyme MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP
-
-
?
additional information
?
-
-
structure-function analysis by hybrid quantum mechanical/molecular mechanical replica path method, three possible reaction pathways via tetrahedral intermediate, overview
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
key role in peptidoglycan biosynthesis
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
-
key role in peptidoglycan biosynthesis
-
-
?
ATP + UDP-N-acetylmuramoyl-L-Ala + Glu
?
-
activity is not in excess in the cell under normal growth conditions, but its amount is adjusted to the requirements of peptidoglycan synthesis
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
-
-
-
?
ATP + UDP-N-acetylmuramyl-L-alanine + D-glutamate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
MurD is essential for cytoplasmic bacterial cell wall biosynthesis
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
ATP binding to the enzyme causes conformational changes, overview
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
potassium phosphate
-
highly dependent on, optimal concentration: 11-16 mM, inhibition above 20 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2R)-2-[((3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(2R)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(2R)-2-[[(7-(2-ethoxy-2-oxoethoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-(3-phenylpropoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-benzyloxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
calculation of binding free energies. Main driving force for binding are non-polar van der Waals-interactions
(2R)-2-[[(7-butoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-pentoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
calculation of binding free energies. Main driving force for binding are non-polar van der Waals-interactions
(2S)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(R,Z)-2-(3-((1-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)formamido)methyl)benzamido)pentanedioic acid
-
(R,Z)-2-(3-((2-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)acetamido)methyl)benzamido)pentanedioic acid
in addition, weak activity against Gram-positive Staphylococcus aureus and Enterococcus faecalis
(R,Z)-2-(3-((3-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)propanamido)methyl)benzamido)pentanedioic acid
in addition, weak activity against Gram-positive Staphylococcus aureus and Enterococcus faecalis
(R,Z)-2-(3-((4-((2,4-dioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
-
(R,Z)-2-(3-((4-((4-oxo-2-thioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
-
2,3,4,5-tetrabromo-6-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic acid
inhibitor identified by structure-based virtual screening
2-((4-[(2S)-butan-2-ylamino]-6-(ethylamino)-1,3,5-triazin-2-yl)sulfanyl)-N-(2-chlorophenyl)acetamide
0.5 mM, 50% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]-5-hydroxybenzoic acid
-
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,4-dicarboxylic acid
-
4-([(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]methyl)-6-(naphthalen-2-ylmethyl)-1,3,5-triazin-2-amine
0.5 mM, 33% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,3-dicarboxylic acid
-
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid
-
6-([(1,1-dioxidotetrahydrothiophen-3-yl)sulfanyl]methyl)-N-(2-phenylethyl)-1,3,5-triazine-2,4-diamine
0.25 mM, 11% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
6-[(1-methyl-1H-imidazol-2-yl)sulfanyl]-N,N'-diphenyl-1,3,5-triazine-2,4-diamine
0.5 mM, 30% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
N-(3-[[(carboxyacetyl)[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]benzoyl)-D-glutamic acid
-
N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid
competitive versus D-Glu, non-competitive versus ATP and UDP-N-acetylmuramoyl-L-Ala
N-(6-butoxy-naphthalene-2-sulfonyl)-L-glutamic acid
competitive versus D-Glu, non-competitive versus UDP-N-acetylmuramoyl-L-Ala
N-[2-fluoro-5-[([4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino)methyl]benzoyl]-D-glutamic acid
-
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 2-nitrobenzenesulfonate
-
71% inhibition at 0.05 mM
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 3-nitrobenzenesulfonate
-
70% inhibition at 0.05 mM
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 4-nitrobenzenesulfonate
-
-
2-([2-(naphthalen-2-ylsulfonyl)hydrazono]methyl)phenyl 2-(benzo[d][1,3]dioxol-5-yl)acetate
-
49% inhibition at 0.10 mM
3-([[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetyl]amino)-4-methylbenzoic acid
-
-
4-cyano-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
78% inhibition at 0.05 mM
benzylidene rhodanines
-
possess MurC inhibitory activity in the low micromolar range
-
beta,gamma-methyleneadenosine 5'-triphosphate
-
nonhydrolyzable ATP analogue
N'-((2-[(2-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
-
N'-((2-[(3-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
70% inhibition at 0.05 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)(2-fluorophenyl)methanesulfonohydrazide
-
39% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)(phenyl)methanesulfonohydrazide
-
58% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
-
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-2-nitrobenzenesulfonohydrazide
-
86% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-3-nitrobenzenesulfonohydrazide
-
74% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)[4-(trifluoromethyl)phenyl]methanesulfonohydrazide
-
57% inhibition at 0.10 mM
N'-((3-[(3-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
61% inhibition at 0.05 mM
N-(2-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-3,5-dinitrobenzamide
-
-
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-2-naphthamide
-
19% inhibition at 0.01 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-3,5-dinitrobenzamide
-
78% inhibition at 0.10 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-4-nitrobenzamide
-
81% inhibition at 0.05 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
56% inhibition at 0.10 mM
N-([(2S)-2-[(2-naphthylsulfonyl)amino]propyl]-sulfonyl)-D-glutamic acid
-
1 mM, 75% residual activity
N-([(2S)-2-[([1,1'-biphenyl]-4-yl-sulfonyl)amino]-propyl]sulfonyl)-D-glutamic acid
-
1 mM, 70% residual activity
N-[((2S)-2-[[(E)-3-(1,3-benzodioxol-5-yl)-2-propenoyl]amino]propyl)sulfonyl]-D-glutamic acid
-
1 mM, 80% residual activity
N-[[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]sulfonyl]-D-glutamic acid
-
1 mM, 74% residual activity
N-[[(2S)-2-([2-[2-(acetylamino)phenoxy]acetyl]-amino)propyl]sulfonyl]-D-glutamic acid
-
1 mM, 93% residual activity
N-[[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-ethyl]sulfonyl]-D-glutamic acid
-
1 mM, 77% residual activity
Phosphinate
-
an analogue of UDP-N-acetylmuramoyl-dipeptide, the N-acetylmuramoyl moiety being replaced by a hexanoyl chain and the peptide bond between L-Ala and D-Glu by a tetrahedral phosphinate bond
potassium phosphate
-
highly dependent on, optimal concentration: 11-16 mM, inhibition above 20 mM, phosphate ion is responsible for inhibition
[1-[(6-Uridinediphospho)hexanamido]ethyl](2,4-dicarboxybutyl)phosphinate pentasodium salt
-
good inhibitor, closely resembles the tetrahedral intermediate that is presumed to form the ligation reaction
(2R)-2-[[(7-(4-cyanobenzyloxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
calculation of binding free energies. Main driving force for binding are non-polar van der Waals-interactions
(2R)-2-[[(7-(4-cyanobenzyloxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
additional information
-
synthesis and evaluation of a series of transition-state analog inhibitors
-
additional information
-
design and synthesis of N-benzylidenesulfonohydrazide inhibitors of MurC as antibacterial agents
-
additional information
-
design of peptidomimetic lead compounds with the ultimate objective of small molecule chemotherapeutic development, affinity selection by immobilized MurD with addition of ATP in an attempt to achieve conformationally homogenous population of target enzymes, overview. No inhibition by peptide MD-C7C_3, i.e. CQSSPHMSC
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
ordered kinetic mechanism
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
turnover of 6.55 at saturation concentrations of all the substrates: 5 mM ATP, 0.25 mM UDP-N-acetylmuramoyl L-alanine, 0.55 mM D-glutamate
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.032
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]-5-hydroxybenzoic acid
pH 8.6, 37°C
0.026
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,4-dicarboxylic acid
pH 8.6, 37°C
0.0058
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,3-dicarboxylic acid
pH 8.6, 37°C
0.125
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid
pH 8.6, 37°C
0.24
N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid
versus D-Glu
0.71
N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid
versus UDP-N-acetylmuramoyl-L-Ala
0.87
N-(6-butoxy-naphthalene-2-sulfonyl)-L-glutamic acid
versus D-Glu
2.13
N-(6-butoxy-naphthalene-2-sulfonyl)-L-glutamic acid
versus UDP-N-acetylmuramoyl-L-Ala
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.089
(2R)-2-[((3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication
0.045
(2R)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication
0.192
(2R)-2-[[(7-(2-ethoxy-2-oxoethoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.132
(2R)-2-[[(7-(3-phenylpropoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.105
(2R)-2-[[(7-(4-cyanobenzyloxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.239
(2R)-2-[[(7-benzyloxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.18
(2R)-2-[[(7-butoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.17
(2R)-2-[[(7-pentoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
Escherichia coli
-
0.01
(2S)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication
0.005
(R,Z)-2-(3-((1-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)formamido)methyl)benzamido)pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication. Malachite green assay in presence of 0.01% Triton X-100
0.003
(R,Z)-2-(3-((2-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)acetamido)methyl)benzamido)pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication. Malachite green assay in presence of 0.01% Triton X-100
0.007
(R,Z)-2-(3-((3-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)propanamido)methyl)benzamido)pentanedioic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication. Malachite green assay in presence of 0.01% Triton X-100
0.085
(R,Z)-2-(3-((4-((2,4-dioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
Escherichia coli
pH 8.0, 37°C
0.045
(R,Z)-2-(3-((4-((4-oxo-2-thioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
Escherichia coli
pH 8.0, 37°C
0.01
2,3,4,5-tetrabromo-6-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic acid
Escherichia coli
pH 8.0, 37°C
0.046
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]-5-hydroxybenzoic acid
Escherichia coli
pH 8.6, 37°C
0.038
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,4-dicarboxylic acid
Escherichia coli
pH 8.6, 37°C
0.0084
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,3-dicarboxylic acid
Escherichia coli
pH 8.6, 37°C
0.182
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid
Escherichia coli
pH 8.6, 37°C
0.015
N-(3-[[(carboxyacetyl)[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]benzoyl)-D-glutamic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication. Malachite green assay in presence of 0.01% Triton X-100
0.252
N-[2-fluoro-5-[([4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino)methyl]benzoyl]-D-glutamic acid
Escherichia coli
pH not specified in the publication, temperature not specified in the publication. Malachite green assay in presence of 0.01% Triton X-100
0.074
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 4-nitrobenzenesulfonate
Escherichia coli
-
pH 8.0, 37°C
0.055
2-bromo-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
Escherichia coli
-
pH 8.0, 37°C
0.105
3-([[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetyl]amino)-4-methylbenzoic acid
Escherichia coli
-
37°C
0.03
3-bromo-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
Escherichia coli
-
pH 8.0, 37°C
0.07
N'-((2-[(2-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
Escherichia coli
-
pH 8.0, 37°C
0.062
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
Escherichia coli
-
pH 8.0, 37°C
0.045
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-2-nitrobenzamide
Escherichia coli
-
pH 8.0, 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala, generating the dipeptide moiety L-Ala-D-Glu in peptidoglycan biosynthesis
additional information
conformational changes of MurD occur upon ligand binding. Upon binding of ATP and UDP-N-acetyl-alpha-D-muramoyl-L-alanine, there is a closing rotation of the C-terminal domain, which does not occur before ATP is bound, targeted molecular dynamics simulation
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
all Mur ligases are topologically similar to each other, extremely flexible, and built of three domains connected by two hinges. Each domain binds one of the three substrates, i.e. ATP, growing nucleotide, or the appropriate amino acid
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of the complexes: MurD-UDP-N-acetylmurmoly-L-alanine -Mg2+ ADP, MurD-UDP-N-acetylmurmoly-L-alanine-D-glutamate and MurD-UDP-N-acetylmurmoly-L-alanine -Mn2+ ADP
crystal structure of the enzyme in presence of its substrate UDP-N-acetylmuramoyl-L-Ala, at 1.9 A resolution
crystal structure of the open enzyme where the C-terminal domain is rotated away from the N-terminal and central domains
crystal structure of the open enzyme where the C-terminal domain is rotated away from the N-terminal and central domains, complexed with UDP-N-acetylmurmoly-L-alanine
in complex with inhibitor 4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid. Only one stereoisomer is seen in the co-crystal structure. The absolute configuration of the crystallised compound is (1R,3R,4S).The carboxyl groups at positions 1 and 3 of the rigid cyclohexyl mimetic of D-glutamic acid occupy exactly the same position as the carboxyl groups of the product UDP-MurNAc-L-Ala-D-Glu. The carboxyl group at position 3 of the cyclohexyl ring of the inhibitor forms a charge-based interaction with N of Lys348, and is additionally hydrogen-bonded with a conserved water molecule, W38, which is further hydrogen-bonded to Ogamma of Thr321 and the carboxyl group of Asp182. The carboxyl group at position 1 of the cyclohexyl ring is held in place by hydrogen bonds with Ogamma of Ser415 and the backbone nitrogen of Phe422. The sulfonic group makes hydrogen bonds with His183 and water molecules W183, W242 and W415
purified free MurD and MurD complexed with the tetrahedral reaction intermediate, hanging drop vapor diffusion method, for free enzyme crystals: mixing of 0.002 ml of 3 mg/ml protein in 20 mM HEPES, pH 5.6, 1 mM DTT, and 1 mM NaN3, with 0.002 ml of reservoir solution containing 1.8 M (NH4)2SO4, 7% v/v 2-methyl-2,4-pentanediol, and 0.1 MMES, pH 5.6, 15°C, 48 h, for complexed enzyme crystals: mixing of 0.002 ml of 4 mg/ml protein in 20 mM HEPES, pH 7.4, 1 mM DTT, 1 mM NaN3, 5 mMAMP-PNP, and 1 mM UDP-N-acetyl-alpha-D-muramoyl-L-alanine, with 0.002 ml of reservoir solution containing 1.8 M Na-malonate, pH 7.0, 15°C, 48 h, X-ray diffraction structure determination and analysis at 1.84-1.90 A resolution
structure of MurD in complex with (R,Z)-2-(3-((4-((2,4-dioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
vapour-diffusion method and hanging-drop system, high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid or N-(6-butoxy-naphthalene-2-sulfonyl)-Lglutamic acid
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 20 mM potassium phosphate, pH 7.0, 1 mM 2-mercaptoethanol, 0.1 mM MgCl2, several months, no loss of activity at high enzyme concentrations: 1-10 mg/ml
-
-20°C, 20 mM potassium phosphate, pH 7.0, 1 mM dithiothreitol, 0.1 mM MgCl2, several months, no loss of activity at high enzyme concentrations: 1-10 mg/ml
-
8°C, 20 mM potassium phosphate, pH 7.0, 1 mM 2-mercaptoethanol, 0.1 mM MgCl2, 1 week, 30% loss of activity
-
8°C, 20 mM potassium phosphate, pH 7.0, 1 mM 2-mercaptoethanol, 0.1 mM MgCl2, sodium Hepes, 1 week, 35-43% loss of activity
-
8°C, 20 mM potassium phosphate, pH 7.0, 1 mM dithiothreitol, 0.1 mM MgCl2, 1 week, 30% loss of activity
-
8°C, 20 mM potassium phosphate, pH 7.0, 1 mM dithiothreitol, 0.1 mM MgCl2, sodium Hepes 1 week, 35-43% loss of activity
-
8°C, 20 mM potassium phosphate, pH 8.0, 1 mM 2-mercaptoethanol, 0.1 mM MgCl2, sodium Hepes, 1 week, 35-43% loss of activity
-
8°C, 20 mM potassium phosphate, pH 8.0, 1 mM dithiothreitol, 0.1 mM MgCl2, sodium Hepes 1 week, 35-43% loss of activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged enzyme from Escherichia coli strain DH5alpha by nickel affinity chromatography and dialysis
method that includes DEAE-Trisacryl M and hydroxyapatite-Ultrogel chromatography. Large-scale purification using 2-mercaptoethanol as a reducing agent, results in 200 mg of purified enzyme from 54 l of culture, adducts with one or two molecules of 2-mercaptoethanol are formed. Replacement of 2-mercaptoethanol by dithiothreitol gave 162 mg of enzyme from 36 l of culture yielding no clusters with the reducing agent.
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene murD, recombinant expression of His6-tagged enzyme in Escherichia coli strain DH5alpha
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
the enzyme is a target in the development of potential antibiotics designed to target the peptidoglycan biosynthetic pathway
analysis
-
assay for monitoring enzyme activity based on the accumulation of adenosine 5'-diphosphate, a product of the reaction catalyzed by MurD ligase, by conversion to a fluorescent signal via a coupled enzyme system, with counterscreen assay to eliminate false positive results
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Mengin-Lecreulx, D.; Flouret, B.; Van Heijenoort, J.
Cytoplasmic steps of peptidoglycan synthesis in Escherichia coli
J. Bacteriol.
151
1109-1117
1982
Escherichia coli
Michaud, C.; Blanot, D.; Flouret, B.; van Heijenoort, J.
Partial purification and specificity studies of the D-glutamate-adding and D-alanyl-D-alanine-adding enzymes from Escherichia coli K12
Eur. J. Biochem.
166
631-637
1987
Escherichia coli
Pratviel-Sosa, F.; Acher, F.; Trigalo, F.; Blanot, D.; Azerad, R.; van Heijenoort, J.
Effect of various analogous of D-glutamic acid on the D-glutamate-adding enzyme from Escherichia coli
FEMS Microbiol. Lett.
115
223-228
1994
Escherichia coli
Ikeda, M.; Wachi, M.; Ishino, F.; Matsuhashi, M.
Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli
Nucleic Acids Res.
18
1058
1990
Escherichia coli
Vaganay, S.; Tanner, M.E.; van Heijenoort, J.; Blanot, D.
Study of the reaction mechanism of the D-glutamic acid-adding enzyme from Escherichia coli
Microb. Drug Resist.
2
51-54
1996
Escherichia coli
Tanner, M.E.; Vaganay, S.; van Heijenoort, J.; Blanot, D.
Phosphinate inhibitors of the D-glutamic acid-adding enzyme of peptidoglycan biosynthesis
J. Org. Chem.
61
1756-1760
1996
Escherichia coli
Bertrand, J.A.; Auger, G.; Fanchon, E.; Martin, L.; Blanot, D.; van Heijenoort, J.; Dideberg, O.
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli
EMBO J.
16
3416-3425
1997
Escherichia coli (P14900), Escherichia coli
Pratviel-Sosa, F.; Mengin-Lecreulx, D.; van Heijenoort, J.
Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli
Eur. J. Biochem.
202
1169-1176
1991
Escherichia coli
Bouhss, A.; Dementin, S.; Parquet, C.; Mengin-Lecreulx, D.; Bertrand, J.A.; Le Beller, D.; Dideberg, O.; van Heijenoort, J.; Blanot, D.
Role of the ortholog and paralog amino acid invariants in the active site of the UDP-MurNAc-L-alanine:D-glutamate ligase (MurD)
Biochemistry
38
12240-12247
1999
Escherichia coli, Escherichia coli DH5-alpha
Gegnas, L.D.; Waddell, S.T.; Chabin, R.M.; Reddy, S.; Wong, K.K.
Inhibitors of the bacterial cell wall biosynthesis enzyme MurD
Bioorg. Med. Chem. Lett.
8
1643-1648
1998
Escherichia coli
Bouhss, A.; Dementin, S.; van Heijenoort, J.; Parquet, C.; Blanot, D.
Formation of adenosine 5'-tetraphosphate from the acyl phosphate intermediate: a difference between the MurC and MurD synthetases of Escherichia coli
FEBS Lett.
453
15-19
1999
Escherichia coli, Escherichia coli JM83(pMLD58)
Bertrand, J.A.; Auger, G.; Martin, L.; Fanchon, E.; Blanot, D.; Le Beller, D.; van Heijenoort, J.; Dideberg, O.
Determination of the MurD mechanism through crystallographic analysis of enzyme complexes
J. Mol. Biol.
289
579-590
1999
Escherichia coli (P14900), Escherichia coli JM83(pMLD58) (P14900)
Bertrand, J.A.; Fanchon, E.; Martin, L.; Chantalat, L.; Auger, G.; Blanot, D.; van Heijenoort, J.; Dideberg, O.
"Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase
J. Mol. Biol.
301
1257-1266
2000
Escherichia coli (P14900), Escherichia coli
Bouhss, A.; Dementin, S.; Van Heijenoort, J.; Parquet, C.; Blanot, D.
MurC and MurD synthetases of peptidoglycan biosynthesis: borohydride trapping of acyl-phosphate intermediates
Methods Enzymol.
354
189-196
2002
Escherichia coli, Escherichia coli JM83(pMLD58)
Auger, G.; Martin, L.; Bertrand, J.; Ferrari, P.; Fanchon, E.; Vaganay, S.; Petillot, Y.; van Heijenoort, J.; Blanot, D.; Dideberg, O.
Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli
Protein Expr. Purif.
13
23-29
1998
Escherichia coli, Escherichia coli JM83(pMLD58)
Kotnik, M.; Humljan, J.; Contreras-Martel, C.; Oblak, M.; Kristan, K.; Herve, M.; Blanot, D.; Urleb, U.; Gobec, S.; Dessen, A.; Solmajer, T.
Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase
J. Mol. Biol.
370
107-115
2007
Escherichia coli (P14900)
Humljan, J.; Kotnik, M.; Boniface, A.; Solmajer, T.; Urleb, U.; Blanot, D.; Gobec, S.
A new approach towards peptidosulfonamides: synthesis of potential inhibitors of bacterial peptidoglycan biosynthesis enzymes MurD and MurE
Tetrahedron
62
10980-10988
2006
Escherichia coli
-
Bratkovic, T.; Lunder, M.; Urleb, U.; Strukelj, B.
Peptide inhibitors of MurD and MurE, essential enzymes of bacterial cell wall biosynthesis
J. Basic Microbiol.
48
202-206
2008
Escherichia coli
Frlan, R.; Kovac, A.; Blanot, D.; Gobec, S.; Pecar, S.; Obreza, A.
Design and synthesis of novel N-benzylidenesulfonohydrazide inhibitors of MurC and MurD as potential antibacterial agents
Molecules
13
11-30
2008
Escherichia coli
Perdih, A.; Hodoscek, M.; Solmajer, T.
MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method
Proteins
15
744-759
2008
Escherichia coli
Turk, S.; Kovac, A.; Boniface, A.; Bostock, J.M.; Chopra, I.; Blanot, D.; Gobec, S.
Discovery of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurF by structure-based virtual screening
Bioorg. Med. Chem.
17
1884-1889
2009
Escherichia coli (P14900)
Kristan, K.; Kotnik, M.; Oblak, M.; Urleb, U.
New high-throughput fluorimetric assay for discovering inhibitors of UDP-N-acetylmuramyl-L-alanine: D-glutamate (MurD) ligase
J. Biomol. Screen.
14
412-418
2009
Escherichia coli
Simcic, M.; Hodoscek, M.; Humljan, J.; Kristan, K.; Urleb, U.; Kocjan, D.; Grdadolnik, S.G.
NMR and molecular dynamics study of the binding mode of naphthalene-N-sulfonyl-D-glutamic acid derivatives: novel MurD ligase inhibitors
J. Med. Chem.
52
2899-2908
2009
Escherichia coli (P14900)
Perdih, A.; Bren, U.; Solmajer, T.
Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase
J. Mol. Model.
15
983-996
2009
Escherichia coli (P14900)
Sosic, I.; Barreteau, H.; Simcic, M.; Sink, R.; Cesar, J.; Zega, A.; Grdadolnik, S.G.; Contreras-Martel, C.; Dessen, A.; Amoroso, A.; Joris, B.; Blanot, D.; Gobec, S.
Second-generation sulfonamide inhibitors of d-glutamic acid-adding enzyme: Activity optimisation with conformationally rigid analogues of D-glutamic acid
Eur. J. Med. Chem.
46
2880-2894
2011
Escherichia coli (P14900)
Tomasic, T.; Kovac, A.; Simcic, M.; Blanot, D.; Grdadolnik, S.G.; Gobec, S.; Kikelj, D.; Peterlin Masic, L.
Novel 2-thioxothiazolidin-4-one inhibitors of bacterial MurD ligase targeting D-Glu- and diphosphate-binding sites
Eur. J. Med. Chem.
46
3964-3975
2011
Escherichia coli (P14900), Escherichia coli
Zidar, N.; Tomasic, T.; Sink, R.; Rupnik, V.; Kovac, A.; Turk, S.; Patin, D.; Blanot, D.; Contreras Martel, C.; Dessen, A.; Mueller Premru, M.; Zega, A.; Gobec, S.; Peterlin Masic, L.; Kikelj, D.
Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase
J. Med. Chem.
53
6584-6594
2010
Escherichia coli (P14900), Escherichia coli
Tomasic, T.; Zidar, N.; Sink, R.; Kovac, A.; Blanot, D.; Contreras-Martel, C.; Dessen, A.; Muller-Premru, M.; Zega, A.; Gobec, S.; Kikelj, D.; Peterlin Masic, L.
Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-l-alanine:d-glutamate ligase (MurD)
J. Med. Chem.
54
4600-4610
2011
Escherichia coli (P14900), Escherichia coli
Tomasic, T.; Kovac, A.; Klebe, G.; Blanot, D.; Gobec, S.; Kikelj, D.; Masic, L.P.
Virtual screening for potential inhibitors of bacterial MurC and MurD ligases
J. Mol. Model.
18
1063-1072
2012
Escherichia coli (P14900)
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