Structure of PDB 5vof Chain H Binding Site BS02

Receptor Information
>5vof Chain H (length=231) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHERQSTRLKMLEVPYVD
RNSCKLSSSFIITQNMFCAGYDTKQEDACQGDAGGPHVTRFKDTYFVTGI
VSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
Ligand information
Ligand IDRIV
InChIInChI=1S/C19H18ClN3O5S/c20-16-6-5-15(29-16)18(25)21-9-14-10-23(19(26)28-14)13-3-1-12(2-4-13)22-7-8-27-11-17(22)24/h1-6,14H,7-11H2,(H,21,25)/t14-/m0/s1
InChIKeyKGFYHTZWPPHNLQ-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1N2CCOCC2=O)N3C[C@@H](OC3=O)CNC(=O)c4ccc(s4)Cl
CACTVS 3.341Clc1sc(cc1)C(=O)NC[C@H]2CN(C(=O)O2)c3ccc(cc3)N4CCOCC4=O
ACDLabs 10.04O=C(NCC3OC(=O)N(c2ccc(N1C(=O)COCC1)cc2)C3)c4sc(Cl)cc4
OpenEye OEToolkits 1.5.0c1cc(ccc1N2CCOCC2=O)N3CC(OC3=O)CNC(=O)c4ccc(s4)Cl
CACTVS 3.341Clc1sc(cc1)C(=O)NC[CH]2CN(C(=O)O2)c3ccc(cc3)N4CCOCC4=O
FormulaC19 H18 Cl N3 O5 S
Name5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide;
Rivaroxaban
ChEMBLCHEMBL198362
DrugBankDB06228
ZINCZINC000003964126
PDB chain5vof Chain H Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vof Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass.
Resolution2.25 Å
Binding residue
(original residue number in PDB)
E97 T98 Y99 F174 A190 V213 W215 G216 G219 G226 I227 Y228
Binding residue
(residue number reindexed from 1)
E83 T84 Y85 F160 A178 V201 W203 G204 G206 G214 I215 Y216
Annotation score1
Binding affinityBindingDB: IC50=700nM,Ki=0.400000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 A195
Catalytic site (residue number reindexed from 1) H42 D88 Q180 G181 D182 A183
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:5vof, PDBe:5vof, PDBj:5vof
PDBsum5vof
PubMed29863725
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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