Structure of PDB 3hpt Chain B Binding Site BS01

Receptor Information
>3hpt Chain B (length=238) 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
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLP
Ligand information
Ligand IDYET
InChIInChI=1S/C23H28N6O3/c1-16-12-17-13-18(7-8-20(17)32-16)26-23(25-15-24)27-19-6-2-3-11-29(22(19)31)14-21(30)28-9-4-5-10-28/h7-8,12-13,19H,2-6,9-11,14H2,1H3,(H2,25,26,27)/t19-/m0/s1
InChIKeyBQUXAJWDRCSKFN-IBGZPJMESA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C2N(CC(=O)N1CCCC1)CCCCC2NC(=N\c4cc3c(oc(c3)C)cc4)/NC#N
CACTVS 3.341Cc1oc2ccc(cc2c1)N=C(NC#N)N[C@H]3CCCCN(CC(=O)N4CCCC4)C3=O
OpenEye OEToolkits 1.5.0Cc1cc2cc(ccc2o1)/N=C(/NC#N)\N[C@H]3CCCCN(C3=O)CC(=O)N4CCCC4
OpenEye OEToolkits 1.5.0Cc1cc2cc(ccc2o1)N=C(NC#N)NC3CCCCN(C3=O)CC(=O)N4CCCC4
CACTVS 3.341Cc1oc2ccc(cc2c1)N=C(NC#N)N[CH]3CCCCN(CC(=O)N4CCCC4)C3=O
FormulaC23 H28 N6 O3
Name1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine
ChEMBLCHEMBL551991
DrugBank
ZINCZINC000043019712
PDB chain3hpt Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3hpt Cyanoguanidine-based lactam derivatives as a novel class of orally bioavailable factor Xa inhibitors.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		T98 Y99 F174 A190 Q192 V213 W215 G216 G218 C220 G226 Y228
Binding residue
(residue number reindexed from 1)		T84 Y85 F162 A180 Q182 V203 W205 G206 G208 C209 G216 Y218
Annotation score1
Binding affinityMOAD: Ki=6.5nM
PDBbind-CN: -logKd/Ki=8.19,Ki=6.5nM
BindingDB: IC50=12nM,Ki=6.5nM
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:3hpt, PDBe:3hpt, PDBj:3hpt
PDBsum3hpt
PubMed19541481
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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