Structure of PDB 1qbv Chain H Binding Site BS03

Receptor Information
>1qbv Chain H (length=249) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
Ligand information
Ligand IDPPX
InChIInChI=1S/C21H27N5O2/c22-18(15-16-5-2-1-3-6-16)21(28)26-14-4-7-19(26)20(27)25-13-12-24-17-8-10-23-11-9-17/h1-3,5-6,8-11,18-19H,4,7,12-15,22H2,(H,23,24)(H,25,27)/t18-,19+/m1/s1
InChIKeyGEIDRYBJURDUSW-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCCNc3ccncc3)N
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCCNc3ccncc3
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCCNc3ccncc3
ACDLabs 12.01O=C(NCCNc1ccncc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.0c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCCNc3ccncc3)N
FormulaC21 H27 N5 O2
Name[PHENYLALANINYL-PROLINYL]-[2-(PYRIDIN-4-YLAMINO)-ETHYL]-AMINE
ChEMBLCHEMBL65273
DrugBankDB08422
ZINCZINC000003871334
PDB chain1qbv Chain H Residue 907 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1qbv Structural analysis of thrombin complexed with potent inhibitors incorporating a phenyl group as a peptide mimetic and aminopyridines as guanidine substitutes.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y60A E97A D189 A190 S195 W215 G216 G219 G226
Binding residue
(residue number reindexed from 1)		Y47 E94 D191 A192 S197 W219 G220 G222 G230
Annotation score1
Binding affinityMOAD: Ki=4100nM
PDBbind-CN: -logKd/Ki=5.39,Ki=4100nM
BindingDB: Ki=4100nM
Enzymatic activity
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1qbv, PDBe:1qbv, PDBj:1qbv
PDBsum1qbv
PubMed9622548
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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