Structure of PDB 2zo3 Chain H Binding Site BS03

Receptor Information
>2zo3 Chain H (length=250) 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
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand ID33U
InChIInChI=1S/C28H31N5O2/c29-25(24(20-8-3-1-4-9-20)21-10-5-2-6-11-21)28(35)33-17-7-12-23(33)27(34)32-18-19-13-15-22(16-14-19)26(30)31/h1-6,8-11,13-16,23-25H,7,12,17-18,29H2,(H3,30,31)(H,32,34)/t23-,25+/m0/s1
InChIKeyODAPDZPYLPTJOD-UKILVPOCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](C(c3ccccc3)c4ccccc4)N)\N
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C4N(C(=O)C(N)C(c2ccccc2)c3ccccc3)CCC4
CACTVS 3.385N[CH](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[CH]3C(=O)NCc4ccc(cc4)C(N)=N
CACTVS 3.385N[C@H](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[C@H]3C(=O)NCc4ccc(cc4)C(N)=N
OpenEye OEToolkits 1.7.5c1ccc(cc1)C(c2ccccc2)C(C(=O)N3CCCC3C(=O)NCc4ccc(cc4)C(=N)N)N
FormulaC28 H31 N5 O2
Namebeta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
ChEMBLCHEMBL1200085
DrugBank
ZINCZINC000013440091
PDB chain2zo3 Chain H Residue 2501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zo3 Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.7 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 V213 W215 G216 E217
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I171 D191 A192 V217 W219 G220 E221
Annotation score1
Binding affinityMOAD: Ki=0.1nM
PDBbind-CN: -logKd/Ki=10.00,Ki=0.1nM
BindingDB: Ki=0.036000nM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2zo3, PDBe:2zo3, PDBj:2zo3
PDBsum2zo3
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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