Structure of PDB 3liw Chain A Binding Site BS03

Receptor Information
>3liw Chain A (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 IDRUP
InChIInChI=1S/C29H37N5O2/c30-26(31)24-8-4-7-20(14-24)15-25(27(35)32-10-9-19-5-2-1-3-6-19)33-28(36)34-29-16-21-11-22(17-29)13-23(12-21)18-29/h1-8,14,21-23,25H,9-13,15-18H2,(H3,30,31)(H,32,35)(H2,33,34,36)/t21-,22+,23-,25-,29-/m1/s1
InChIKeyQYKLXCYULDLMPX-ZEFMGYOLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCNC(=O)C(Cc2cccc(c2)C(=N)N)NC(=O)NC34CC5CC(C3)CC(C5)C4
CACTVS 3.341NC(=N)c1cccc(C[CH](NC(=O)NC23CC4CC(CC(C4)C2)C3)C(=O)NCCc5ccccc5)c1
CACTVS 3.341NC(=N)c1cccc(C[C@@H](NC(=O)NC23CC4CC(CC(C4)C2)C3)C(=O)NCCc5ccccc5)c1
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCNC(=O)[C@@H](Cc2cccc(c2)C(=N)N)NC(=O)NC34CC5CC(C3)CC(C5)C4
ACDLabs 10.04O=C(NCCc1ccccc1)C(NC(=O)NC23CC4CC(C2)CC(C3)C4)Cc5cc(C(=[N@H])N)ccc5
FormulaC29 H37 N5 O2
Name(R)-2-(3-ADAMANTAN-1-YL-UREIDO)-3-(3-CARBAMIMIDOYL-PHENYL)-N-PHENETHYL-PROPIONAMIDE
ChEMBL
DrugBank
ZINC
PDB chain3liw Chain A Residue 1 [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]
PDB3liw (R)-3-Amidinophenylalanine-Derived Inhibitors of Factor Xa with a Novel Active-Site Binding Mode
Resolution2.22 Å
Binding residue
(original residue number in PDB)		Y99 R143 E146 F174 D189 A190 C191 Q192 W215 G216 G218 C220
Binding residue
(residue number reindexed from 1)		Y85 R132 E135 F162 D179 A180 C181 Q182 W205 G206 G208 C209
Annotation score1
Binding affinityMOAD: Ki=0.025uM
PDBbind-CN: -logKd/Ki=7.60,Ki=0.025uM
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:3liw, PDBe:3liw, PDBj:3liw
PDBsum3liw
PubMed12437104
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

[Back to BioLiP]