Structure of PDB 2y5h Chain A Binding Site BS01

Receptor Information
>2y5h Chain A (length=233) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGEQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
Ligand information
Ligand IDY5H
InChIInChI=1S/C22H28ClN4O3S/c1-27(2,3)11-5-10-26-21(28)17-14-6-4-9-25(14)19(18(17)22(26)29)13-12-30-20(24-13)15-7-8-16(23)31-15/h7-8,12,14,17-19H,4-6,9-11H2,1-3H3/q+1/t14-,17-,18-,19-/m0/s1
InChIKeyJCNHSXPHCSYYCR-QZHFEQFPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCC[N@@]3[C@H]([C@H]2C1=O)c4coc(n4)c5ccc(s5)Cl
OpenEye OEToolkits 1.6.1C[N+](C)(C)CCCN1C(=O)C2C3CCCN3C(C2C1=O)c4coc(n4)c5ccc(s5)Cl
CACTVS 3.352C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4coc(n4)c5sc(Cl)cc5
CACTVS 3.352C[N+](C)(C)CCCN1C(=O)[CH]2[CH]3CCCN3[CH]([CH]2C1=O)c4coc(n4)c5sc(Cl)cc5
FormulaC22 H28 Cl N4 O3 S
Name3-[(3AS,4R,5S,8AS,8BR)-4-[2-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-4-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM
ChEMBLCHEMBL4294106
DrugBank
ZINCZINC000082874039
PDB chain2y5h Chain A Residue 1244 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y5h Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water.
Resolution1.33 Å
Binding residue
(original residue number in PDB)		T98 Y99 F174 A190 Q192 V213 W215 G216 C220 G226 I227
Binding residue
(residue number reindexed from 1)		T84 Y85 F162 A180 Q182 V203 W205 G206 C209 G216 I217
Annotation score1
Binding affinityMOAD: Ki=1620nM
PDBbind-CN: -logKd/Ki=5.79,Ki=1620nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:2y5h, PDBe:2y5h, PDBj:2y5h
PDBsum2y5h
PubMed22162109
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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