Structure of PDB 2bmg Chain B Binding Site BS02

Receptor Information
>2bmg Chain B (length=234) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT
Ligand information
Ligand IDI1H
InChIInChI=1S/C27H29Cl2N3O3/c1-34-25-5-3-21(16-26(25)35-15-10-20-2-4-22(28)17-24(20)29)27(33)31-18-19-8-13-32(14-9-19)23-6-11-30-12-7-23/h2-7,11-12,16-17,19H,8-10,13-15,18H2,1H3,(H,31,33)
InChIKeyUVSAHJWEJXWVGO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc1ccc(c(Cl)c1)CCOc2c(OC)ccc(c2)C(=O)NCC4CCN(c3ccncc3)CC4
OpenEye OEToolkits 1.5.0COc1ccc(cc1OCCc2ccc(cc2Cl)Cl)C(=O)NCC3CCN(CC3)c4ccncc4
CACTVS 3.341COc1ccc(cc1OCCc2ccc(Cl)cc2Cl)C(=O)NCC3CCN(CC3)c4ccncc4
FormulaC27 H29 Cl2 N3 O3
Name3-[2-(2,4-DICHLOROPHENYL)ETHOXY]-4-METHOXY-N-[(1-PYRIDIN-4-YLPIPERIDIN-4-YL)METHYL]BENZAMIDE
ChEMBLCHEMBL96434
DrugBank
ZINCZINC000013643398
PDB chain2bmg Chain B Residue 1246 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2bmg Structural Requirements for Factor Xa Inhibition by 3-Oxybenzamides with Neutral P1 Substituents: Combining X-Ray Crystallography, 3D-Qsar and Tailored Scoring Functions
Resolution2.7 Å
Binding residue
(original residue number in PDB)		T98 Y99 F174 D189 A190 C191 W215 G216 G219 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		T84 Y85 F162 D179 A180 C181 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.74,Ki=18nM
BindingDB: Ki=18nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D88 Q182 G183 D184 S185 G186
Enzyme Commision number 3.4.21.6: coagulation factor Xa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2bmg, PDBe:2bmg, PDBj:2bmg
PDBsum2bmg
PubMed15857135
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

[Back to BioLiP]