Structure of PDB 1nfy Chain A Binding Site BS02

Receptor Information
>1nfy 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 IDRTR
InChIInChI=1S/C20H19ClN4O3S2/c21-16-6-5-15-9-19(29-17(15)10-16)30(27,28)25-8-7-24(18(26)12-25)11-13-1-3-14(4-2-13)20(22)23/h1-6,9-10H,7-8,11-12H2,(H3,22,23)
InChIKeyVXONTEUOQXFJJS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C2N(Cc1ccc(C(=[N@H])N)cc1)CCN(C2)S(=O)(=O)c4sc3cc(Cl)ccc3c4
OpenEye OEToolkits 1.5.0c1cc(ccc1CN2CCN(CC2=O)S(=O)(=O)c3cc4ccc(cc4s3)Cl)C(=N)N
OpenEye OEToolkits 1.5.0c1cc(ccc1CN2CC[N@@](CC2=O)S(=O)(=O)c3cc4ccc(cc4s3)Cl)C(=N)N
CACTVS 3.341NC(=N)c1ccc(CN2CCN(CC2=O)[S](=O)(=O)c3sc4cc(Cl)ccc4c3)cc1
FormulaC20 H19 Cl N4 O3 S2
Name4-({4-[(6-CHLORO-1-BENZOTHIEN-2-YL)SULFONYL]-2-OXOPIPERAZIN-1-YL}METHYL)BENZENECARBOXIMIDAMIDE
ChEMBLCHEMBL48813
DrugBankDB08495
ZINCZINC000002047636
PDB chain1nfy 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

[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]
PDB1nfy Molecular structures of human Factor Xa complexed with ketopiperazine inhibitors: preference for a neutral group in the S1 pocket.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y99 F174 D189 A190 Q192 V213 W215 G216 G218 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		Y85 F162 D179 A180 Q182 V203 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityMOAD: Ki=1.3nM
PDBbind-CN: -logKd/Ki=8.89,Ki=1.3nM
BindingDB: Ki=1.3nM
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:1nfy, PDBe:1nfy, PDBj:1nfy
PDBsum1nfy
PubMed12593649
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

[Back to BioLiP]