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Structure of PDB 1ksn Chain A Binding Site BS02

Receptor Information
>1ksn 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 IDFXV
InChIInChI=1S/C25H26N4O4/c1-16(22(25(31)33-2)15-17-4-3-5-21(14-17)23(26)27)28-24(30)20-8-6-18(7-9-20)19-10-12-29(32)13-11-19/h3-14,16,22H,15H2,1-2H3,(H3,26,27)(H,28,30)/p+1/t16-,22-/m1/s1
InChIKeyPFGVNLZDWRZPJW-OPAMFIHVSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(OC)C(Cc1cc(C(=[NH2+])\N)ccc1)C(NC(=O)c3ccc(c2cc[n+]([O-])cc2)cc3)C
OpenEye OEToolkits 1.5.0CC(C(Cc1cccc(c1)C(=[NH2+])N)C(=O)OC)NC(=O)c2ccc(cc2)c3cc[n+](cc3)[O-]
CACTVS 3.341COC(=O)[C@H](Cc1cccc(c1)C(N)=[NH2+])[C@@H](C)NC(=O)c2ccc(cc2)c3cc[n+]([O-])cc3
CACTVS 3.341COC(=O)[CH](Cc1cccc(c1)C(N)=[NH2+])[CH](C)NC(=O)c2ccc(cc2)c3cc[n+]([O-])cc3
OpenEye OEToolkits 1.5.0C[C@H]([C@@H](Cc1cccc(c1)C(=[NH2+])N)C(=O)OC)NC(=O)c2ccc(cc2)c3cc[n+](cc3)[O-]
FormulaC25 H27 N4 O4
NameMETHYL-3-(4'-N-OXOPYRIDYLPHENOYL)-3-METHYL-2-(M-AMIDINOBENZYL)-PROPIONATE;
FXV673
ChEMBL
DrugBank
ZINC
PDB chain1ksn Chain A Residue 401 [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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PDB1ksn Optimization of the beta-aminoester class of factor Xa inhibitors. Part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 E147 F174 D189 A190 C191 Q192 S195 V213 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 E135 F162 D179 A180 C181 Q182 S185 V203 W205 G206 G208 C209
Annotation score1
Binding affinityMOAD: Ki=0.4nM
PDBbind-CN: -logKd/Ki=9.40,Ki=0.4nM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1ksn, PDBe:1ksn, PDBj:1ksn
PDBsum1ksn
PubMed12039587
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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