Structure of PDB 2zda Chain H Binding Site BS03

Receptor Information
>2zda Chain H (length=251) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G
Ligand information
Ligand ID32U
InChIInChI=1S/C22H27N5O2/c23-18(13-15-5-2-1-3-6-15)22(29)27-12-4-7-19(27)21(28)26-14-16-8-10-17(11-9-16)20(24)25/h1-3,5-6,8-11,18-19H,4,7,12-14,23H2,(H3,24,25)(H,26,28)/p+1/t18-,19+/m1/s1
InChIKeyVZFTWWJAUZOJDH-MOPGFXCFSA-O
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(cc3)C(N)=[NH2+]
ACDLabs 12.01O=C(NCc1ccc(C(=[NH2+])\\N)cc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=[NH2+]
OpenEye OEToolkits 1.7.5c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(cc3)C(=[NH2+])N)N
OpenEye OEToolkits 1.7.5c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(=[NH2+])N)N
FormulaC22 H28 N5 O2
NameD-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide
ChEMBL
DrugBankDB07005
ZINC
PDB chain2zda Chain H Residue 1000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2zda Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.73 Å
Binding residue
(original residue number in PDB)		Y60A L99 I174 D189 A190 V213 W215 G216
Binding residue
(residue number reindexed from 1)		Y47 L96 I172 D192 A193 V218 W220 G221
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.40,Ki=4nM
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:2zda, PDBe:2zda, PDBj:2zda
PDBsum2zda
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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