Structure of PDB 5k0h Chain A Binding Site BS03

Receptor Information
>5k0h 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 ID6PK
InChIInChI=1S/C27H31N5O5S/c28-26(29)23-13-11-20(12-14-23)15-30-25(33)16-31-27(34)24(18-37-17-21-7-3-1-4-8-21)32-38(35,36)19-22-9-5-2-6-10-22/h1-14,24,32H,15-19H2,(H3,28,29)(H,30,33)(H,31,34)/t24-/m1/s1
InChIKeyRXJPCNAPBKYKMA-XMMPIXPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)COCC(C(=O)NCC(=O)NCc2ccc(cc2)C(=N)N)NS(=O)(=O)Cc3ccccc3
CACTVS 3.385NC(=N)c1ccc(CNC(=O)CNC(=O)[CH](COCc2ccccc2)N[S](=O)(=O)Cc3ccccc3)cc1
CACTVS 3.385NC(=N)c1ccc(CNC(=O)CNC(=O)[C@@H](COCc2ccccc2)N[S](=O)(=O)Cc3ccccc3)cc1
ACDLabs 12.01c3ccc(CS(=O)(NC(C(=O)NCC(NCc1ccc(\C(=N)N)cc1)=O)COCc2ccccc2)=O)cc3
OpenEye OEToolkits 2.0.4[H]/N=C(\c1ccc(cc1)CNC(=O)CNC(=O)[C@@H](COCc2ccccc2)NS(=O)(=O)Cc3ccccc3)/N
FormulaC27 H31 N5 O5 S
NameO-benzyl-N-(benzylsulfonyl)-D-seryl-N-[(4-carbamimidoylphenyl)methyl]glycinamide
ChEMBLCHEMBL4238121
DrugBank
ZINCZINC000138128932
PDB chain5k0h Chain A Residue 303 [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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PDB5k0h New substrate analogue inhibitors of factor Xa containing 4-amidinobenzylamide as P1 residue: part 1.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 R143 E147 F174 D189 A190 C191 Q192 S195 V213 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 R132 E135 F162 D179 A180 C181 Q182 S185 V203 W205 G206 G208 C209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.09,Ki=0.081uM
BindingDB: Ki=29nM
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:5k0h, PDBe:5k0h, PDBj:5k0h
PDBsum5k0h
PubMed16848746
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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