Structure of PDB 3m37 Chain A Binding Site BS01

Receptor Information
>3m37 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 IDM37
InChIInChI=1S/C24H19F4N5O3S/c25-17-11-14(16-6-2-4-8-21(16)37(30,35)36)9-10-18(17)31-23(34)20-12-22(24(26,27)28)32-33(20)19-7-3-1-5-15(19)13-29/h1-12H,13,29H2,(H,31,34)(H2,30,35,36)
InChIKeyTYPXEIGMGZWOGB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(c(c1)CN)n2c(cc(n2)C(F)(F)F)C(=O)Nc3ccc(cc3F)c4ccccc4S(=O)(=O)N
CACTVS 3.370NCc1ccccc1n2nc(cc2C(=O)Nc3ccc(cc3F)c4ccccc4[S](N)(=O)=O)C(F)(F)F
ACDLabs 12.01O=S(=O)(N)c1ccccc1c2ccc(c(F)c2)NC(=O)c4cc(nn4c3c(cccc3)CN)C(F)(F)F
FormulaC24 H19 F4 N5 O3 S
Name1-[2-(aminomethyl)phenyl]-N-(3-fluoro-2'-sulfamoylbiphenyl-4-yl)-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide
ChEMBLCHEMBL151939
DrugBank
ZINC
PDB chain3m37 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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PDB3m37 Discovery of 1-(2-Aminomethylphenyl)-3-trifluoromethyl-N-[3-fluoro-2'-(aminosulfonyl)[1,1'-biphenyl)]-1H-pyrazole-5-carboxyamide (DPC602), a Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K96 E97 T98 Y99 E146 F174 A190 C191 Q192 S195 W215 G216 G218 C220
Binding residue
(residue number reindexed from 1)		K82 E83 T84 Y85 E135 F162 A180 C181 Q182 S185 W205 G206 G208 C209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.04,Ki=0.91nM
BindingDB: Ki=0.910nM
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
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Biological Process
External links
PDB RCSB:3m37, PDBe:3m37, PDBj:3m37
PDBsum3m37
PubMed14640539
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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