Structure of PDB 1nfu Chain A Binding Site BS02

Receptor Information
>1nfu 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 IDRRP
InChIInChI=1S/C20H19ClN4O3S2/c21-16-5-4-14-9-19(29-17(14)10-16)30(27,28)25-7-6-24(18(26)12-25)11-13-2-1-3-15(8-13)20(22)23/h1-5,8-10H,6-7,11-12H2,(H3,22,23)
InChIKeyPRMSFVUWLBPPLY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=N)N)CN2CC[N@@](CC2=O)S(=O)(=O)c3cc4ccc(cc4s3)Cl
ACDLabs 10.04O=C2N(Cc1cc(C(=[N@H])N)ccc1)CCN(C2)S(=O)(=O)c4sc3cc(Cl)ccc3c4
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=N)N)CN2CCN(CC2=O)S(=O)(=O)c3cc4ccc(cc4s3)Cl
CACTVS 3.341NC(=N)c1cccc(CN2CCN(CC2=O)[S](=O)(=O)c3sc4cc(Cl)ccc4c3)c1
FormulaC20 H19 Cl N4 O3 S2
Name3-({4-[(6-CHLORO-1-BENZOTHIEN-2-YL)SULFONYL]-2-OXOPIPERAZIN-1-YL}METHYL)BENZENECARBOXIMIDAMIDE
ChEMBLCHEMBL351298
DrugBankDB08487
ZINCZINC000002047642
PDB chain1nfu Chain A Residue 301 [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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PDB1nfu Molecular structures of human Factor Xa complexed with ketopiperazine inhibitors: preference for a neutral group in the S1 pocket.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		F174 D189 A190 C191 Q192 V213 W215 G216 E217 G219 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		F162 D179 A180 C181 Q182 V203 W205 G206 E207 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityMOAD: Ki=18nM
PDBbind-CN: -logKd/Ki=7.74,Ki=18nM
BindingDB: Ki=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
View graph for
Biological Process
External links
PDB RCSB:1nfu, PDBe:1nfu, PDBj:1nfu
PDBsum1nfu
PubMed12593649
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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