Structure of PDB 1lqd Chain B Binding Site BS02

Receptor Information
>1lqd 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 IDCMI
InChIInChI=1S/C27H28N4O/c1-17-10-18(2)12-21(11-17)15-30-27(32)25-14-23-19(3)6-4-9-24(23)31(25)16-20-7-5-8-22(13-20)26(28)29/h4-14H,15-16H2,1-3H3,(H3,28,29)(H,30,32)
InChIKeyJSQZLEYFOOSZPU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NCc1cc(cc(c1)C)C)c3cc2c(cccc2n3Cc4cc(C(=[N@H])N)ccc4)C
OpenEye OEToolkits 1.5.0[H]/N=C(\c1cccc(c1)Cn2c3cccc(c3cc2C(=O)NCc4cc(cc(c4)C)C)C)/N
OpenEye OEToolkits 1.5.0[H]N=C(c1cccc(c1)Cn2c3cccc(c3cc2C(=O)NCc4cc(cc(c4)C)C)C)N
CACTVS 3.341Cc1cc(C)cc(CNC(=O)c2cc3c(C)cccc3n2Cc4cccc(c4)C(N)=N)c1
FormulaC27 H28 N4 O
Name1-(3-CARBAMIMIDOYL-BENZYL)-4-METHYL-1H-INDOLE-2-CARBOXYLIC ACID 3,5-DIMETHYL-BENZYLAMIDE
ChEMBLCHEMBL93087
DrugBank
ZINCZINC000001490443
PDB chain1lqd 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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PDB1lqd Design and Quantitative Structure-Activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D189 A190 C191 Q192 W215 G216 C220 G226
Binding residue
(residue number reindexed from 1)		D179 A180 C181 Q182 W205 G206 C209 G216
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.05,Ki=9nM
BindingDB: Ki=9nM
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:1lqd, PDBe:1lqd, PDBj:1lqd
PDBsum1lqd
PubMed12061878
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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