Structure of PDB 2zgx Chain H Binding Site BS03

Receptor Information
>2zgx 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 ID29U
InChIInChI=1S/C17H25N5O2/c1-2-13(18)17(24)22-9-3-4-14(22)16(23)21-10-11-5-7-12(8-6-11)15(19)20/h5-8,13-14H,2-4,9-10,18H2,1H3,(H3,19,20)(H,21,23)/t13-,14+/m1/s1
InChIKeyYHAMQFKGUUSJMU-KGLIPLIRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[C@@H](N)C(=O)N1CCC[C@H]1C(=O)NCc2ccc(cc2)C(N)=N
OpenEye OEToolkits 1.7.5CCC(C(=O)N1CCCC1C(=O)NCc2ccc(cc2)C(=N)N)N
ACDLabs 10.04O=C(NCc1ccc(C(=[N@H])N)cc1)C2N(C(=O)C(N)CC)CCC2
CACTVS 3.385CC[CH](N)C(=O)N1CCC[CH]1C(=O)NCc2ccc(cc2)C(N)=N
OpenEye OEToolkits 1.7.5[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC)N)\N
FormulaC17 H25 N5 O2
Name1-[(2R)-2-aminobutanoyl]-N-(4-carbamimidoylbenzyl)-L-prolinamide
ChEMBLCHEMBL1198148
DrugBankDB06947
ZINCZINC000039024957
PDB chain2zgx Chain H Residue 1601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zgx Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D D189 A190 V213 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 D191 A192 V217 W219 G220
Annotation score1
Binding affinityMOAD: Ki=180nM
PDBbind-CN: -logKd/Ki=6.74,Ki=180nM
BindingDB: Ki=180nM,Kd=110nM
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:2zgx, PDBe:2zgx, PDBj:2zgx
PDBsum2zgx
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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