Structure of PDB 3k9x Chain D Binding Site BS01

Receptor Information
>3k9x Chain D (length=238) 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
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLP
Ligand information
Ligand IDMBM
InChIInChI=1S/C28H32N6O4/c1-19-15-21-16-22(9-10-24(21)38-19)30-28(32-26(36)20-7-6-11-29-17-20)31-23-8-2-3-14-34(27(23)37)18-25(35)33-12-4-5-13-33/h6-7,9-11,15-17,23H,2-5,8,12-14,18H2,1H3,(H2,30,31,32,36)/t23-/m0/s1
InChIKeyGNYXHJVKEWBHAI-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Cc1oc2ccc(cc2c1)N=C(N[C@H]3CCCCN(CC(=O)N4CCCC4)C3=O)NC(=O)c5cccnc5
ACDLabs 11.02O=C2N(CC(=O)N1CCCC1)CCCCC2N/C(=N\c4cc3c(oc(c3)C)cc4)NC(=O)c5cccnc5
OpenEye OEToolkits 1.7.0Cc1cc2cc(ccc2o1)N=C(NC3CCCCN(C3=O)CC(=O)N4CCCC4)NC(=O)c5cccnc5
OpenEye OEToolkits 1.7.0Cc1cc2cc(ccc2o1)/N=C(\N[C@H]3CCCCN(C3=O)CC(=O)N4CCCC4)/NC(=O)c5cccnc5
CACTVS 3.352Cc1oc2ccc(cc2c1)N=C(N[CH]3CCCCN(CC(=O)N4CCCC4)C3=O)NC(=O)c5cccnc5
FormulaC28 H32 N6 O4
NameN-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide
ChEMBLCHEMBL567904
DrugBank
ZINCZINC000044460288
PDB chain3k9x Chain D Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3k9x Aroylguanidine-based factor Xa inhibitors: the discovery of BMS-344577
Resolution1.9 Å
Binding residue
(original residue number in PDB)		T98 Y99 E147 F174 A190 C191 Q192 V213 W215 G216 G218 C220 G226 Y228
Binding residue
(residue number reindexed from 1)		T84 Y85 E135 F162 A180 C181 Q182 V203 W205 G206 G208 C209 G216 Y218
Annotation score1
Binding affinityMOAD: ic50=4nM
BindingDB: IC50=4nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3k9x, PDBe:3k9x, PDBj:3k9x
PDBsum3k9x
PubMed19896847
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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