EC Number   |
|---|
   3.4.21.6 | 20 ns of molecular dynamics and steered molecular dynamics simulations on open and closed conformation, based on crystal structure PBD entry 1C5M. Interchangeable conformational transition between open and closed form. The opening and closing dynamics of the FXa subsites involve potential mechanistic roles of residues Glu97, Lys96, and aromatic-aromatic interactions of various aromatic residues His57, Tyr60, Phe94, Tyr99, Phe194, and Trp215 |
| 3.4.21.6 | chymotrypsin treated factor Xa, i.e. des-Gla(1-44), lacking the Gla domain, free or complexed with inhibitor BIBT0871, 3 mg/ml protein in 10 mM Tris-HCl, pH 7.5, 20 mM sodium chloride, 2 mM calcium chloride, equilibrated against 20% PEG 4000, 0.1 M malate/imidazole, 0.1 M sodium acetate, pH 6.0, some days, X-ray diffraction structure determination and analysis at 1.9-3.0 A, cocrystallization of factor Xa complexed with thrombin and inhibitor BIBR1109 |
| 3.4.21.6 | complex between the enzyme from which the residues 1-44 of the light chain have been removed and the inhibitor (2RS)-(3'-amidino-3-biphenyl)-5-(4-pyridylamino)pentanoic acid |
| 3.4.21.6 | in complex with inhibitor 1-(4-methoxyphenyl)-6-[4-[1-(pyrrolidin-1-ylmethyl)cyclopropyl]phenyl]-3-(trifluoromethyl)-1,4,5,6-tetrahydro-7H-pyrazolo[3,4-c]pyridin-7-one to 2.0 A resolution. The molecule adopts an extended binding mode with the para-methoxyphenyl group located in the S1 pocket and the alpha-CH2-N-pyrrolidinyl phenylcyclopropyl group occupying the S4 pocket |
| 3.4.21.6 | in complex with inhibitor N-[(1R,2S,5S)-2-[[(5-chloroindol-2-yl)carbonyl]amino]-5-(dimethylcarbamoyl)cyclohexyl]-5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine-2-carboxamide hydrochloride, to 2.1 A resolution |
| 3.4.21.6 | method for quantifying the contributions to the free energy of binding due to the ligand evacuating energetically unfavorable and entropically structured solvent for the set of congeneric pairs. The expulsion of active-site water strongly impacts protein-ligand binding affinities in two ways. Hydrophobic ligand groups that displace water from energetically unfavorable hydrophobically enclosed environments contribute enthalpically since the water molecules will make more favorable interactions in the bulk fluid. Ligand groups that displace entropically structured solvent contribute even when the solvent interacts favorably with the protein since well-designed ligands will recapture the protein-water interaction energy |
| 3.4.21.6 | molecular modeling of complex with inhibitor [5-(4-[3-[(6-chloronaphthalen-2-yl)sulfonyl]propanoyl]piperazin-1-yl)imidazo[1,2-a]pyridin-2-yl]methanol. The imidazo[1,2-a]pyridine ring is deeply buried inside the hydrophobic S4 site and makes hydrophobic contacts with the aromatic rings of Tyr99, Phe174, and Trp215 without the salt bridge with any amino acid residue in this site. The imidazo[1,2-a]pyridine ring extends across the face of the Phe174 phenyl ring with a favorable pi-pi stacking interaction |
| 3.4.21.6 | purified chymotrypsin treated enzyme lacking the first 45 amino acid residues, i.e. des(1-45)FXa, complexed with inhibitor, 8 mg/ml protein in 5 mM MES-NaOH, pH 6.0, 5 mM CaCl2, 0.001 mM inhibitor RPR128515, 0.003 ml mixed with equal volume of reservoir solution containing 18-20% PEG 600, 50 mM MES-NaOH, pH 5.7, hanging drop vapour diffusion method, 19°C, a few days, X-ray duffraction structure determination and analysis at 2.1 A resolution of crystals soaked in mother liquor containing 1-1.5 mM inhibitor and 5-10% dimethylformamide |
| 3.4.21.6 | purified chymotrypsin-treated enzyme, i.e. des-Gla-factor Xa, complexed with inhibitor (R)-2-(3-adamant-1-yl-ureido)-3-(3-carbimidoylphenyl)-N-phenethyl-propionamide, 20°C, hanging drop vapour diffusion technique, from 0.1 M MES-OH, pH 5.8, 10 mM CaCl2, 18% PEG 6000, 10 mM inhibitor, enlarged by seeding, X-ray diffraction structure determination and analysis at 2.22 A resolution |
| 3.4.21.6 | purified factor Xa, 8 mg/ml, in MES-NaOH, pH 6.0, 5 mM CaCl2, 0.001 mM inhibitor RPR128515, hanging drop vapour diffusion method, equal volume of 0.003 ml of protein and reservoir solution, the latter containing 18-20% PEG 600, 50 mM MES-NaOH, pH 5.7, 19°C, a few days, seeding cycles are necessary to improve size and shape of the crystals, X-ray diffraction structure determination and analysis at 2.1 A resolution |
