Structure of PDB 1lpz Chain B Binding Site BS02

Receptor Information
>1lpz 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 IDCMB
InChIInChI=1S/C25H22Cl2N4O/c1-15-4-2-7-22-21(15)12-23(25(32)30-13-17-9-19(26)11-20(27)10-17)31(22)14-16-5-3-6-18(8-16)24(28)29/h2-12H,13-14H2,1H3,(H3,28,29)(H,30,32)
InChIKeyYAAKSJLUBVPBIM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1Cc1cccc2c1cc(n2Cc3cccc(c3)C(=N)N)C(=O)NCc4cc(cc(c4)Cl)Cl
CACTVS 3.352Cc1cccc2n(Cc3cccc(c3)C(N)=N)c(cc12)C(=O)NCc4cc(Cl)cc(Cl)c4
FormulaC25 H22 Cl2 N4 O
Name1-(3-carbamimidoylbenzyl)-N-(3,5-dichlorobenzyl)-4-methyl-1H-indole-2-carboxamide
ChEMBLCHEMBL92776
DrugBank
ZINCZINC000002047778
PDB chain1lpz 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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PDB1lpz Design and Quantitative Structure-Activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa
Resolution2.4 Å
Binding residue
(original residue number in PDB)		T98 Y99 R143 D189 A190 C191 Q192 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		T84 Y85 R132 D179 A180 C181 Q182 W205 G206 G208 C209
Annotation score1
Binding affinityMOAD: Ki=25nM
PDBbind-CN: -logKd/Ki=7.60,Ki=25nM
BindingDB: Ki=25nM
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:1lpz, PDBe:1lpz, PDBj:1lpz
PDBsum1lpz
PubMed12061878
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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