Structure of PDB 1lpk Chain B Binding Site BS02

Receptor Information
>1lpk Chain B (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 IDCBB
InChIInChI=1S/C25H23N5O2/c26-23(27)19-8-3-5-16(11-19)14-30-21-10-2-1-7-18(21)13-22(30)25(31)32-15-17-6-4-9-20(12-17)24(28)29/h1-13H,14-15H2,(H3,26,27)(H3,28,29)
InChIKeyZJZBBFMRHRUCQD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=N)c1cccc(COC(=O)c2cc3ccccc3n2Cc4cccc(c4)C(N)=N)c1
OpenEye OEToolkits 2.0.7[H]/N=C(/c1cccc(c1)Cn2c3ccccc3cc2C(=O)OCc4cccc(c4)/C(=N\[H])/N)\N
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cc(n2Cc3cccc(c3)C(=N)N)C(=O)OCc4cccc(c4)C(=N)N
FormulaC25 H23 N5 O2
Name1-(3-CARBAMIMIDOYL-BENZYL)-1H-INDOLE-2-CARBOXYLIC ACID 3-CARBAMIMIDOYL-BENZYLESTER;
(3-carbamimidoylphenyl)methyl 1-[(3-carbamimidoylphenyl)methyl]indole-2-carboxylate
ChEMBLCHEMBL92836
DrugBank
ZINCZINC000002047781
PDB chain1lpk Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1lpk Design and Quantitative Structure-Activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R143 F174 D189 A190 C191 Q192 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		R132 F162 D179 A180 C181 Q182 W205 G206 G208 C209
Annotation score1
Binding affinityMOAD: Ki=28nM
PDBbind-CN: -logKd/Ki=7.55,Ki=28nM
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:1lpk, PDBe:1lpk, PDBj:1lpk
PDBsum1lpk
PubMed12061878
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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