Structure of PDB 2zfp Chain H Binding Site BS03

Receptor Information
>2zfp 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 ID19U
InChIInChI=1S/C16H22ClN3O2/c1-2-13(18)16(22)20-8-4-7-14(20)15(21)19-10-11-5-3-6-12(17)9-11/h3,5-6,9,13-14H,2,4,7-8,10,18H2,1H3,(H,19,21)/t13-,14+/m1/s1
InChIKeyOTYYXGRJXJFTCD-KGLIPLIRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCc1cccc(Cl)c1)C2N(C(=O)C(N)CC)CCC2
OpenEye OEToolkits 1.7.6CC[C@H](C(=O)N1CCC[C@H]1C(=O)NCc2cccc(c2)Cl)N
OpenEye OEToolkits 1.7.6CCC(C(=O)N1CCCC1C(=O)NCc2cccc(c2)Cl)N
CACTVS 3.370CC[C@@H](N)C(=O)N1CCC[C@H]1C(=O)NCc2cccc(Cl)c2
CACTVS 3.370CC[CH](N)C(=O)N1CCC[CH]1C(=O)NCc2cccc(Cl)c2
FormulaC16 H22 Cl N3 O2
Name1-[(2R)-2-aminobutanoyl]-N-(3-chlorobenzyl)-L-prolinamide
ChEMBLCHEMBL1198130
DrugBankDB06878
ZINCZINC000039024307
PDB chain2zfp Chain H Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2zfp Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution2.25 Å
Binding residue
(original residue number in PDB)		H57 Y60A A190 S195 V213 S214 W215 G216 G226 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 A193 S198 V218 S219 W220 G221 G231 F232
Annotation score1
Binding affinityMOAD: Ki=6.8uM
PDBbind-CN: -logKd/Ki=5.17,Ki=6.8uM
BindingDB: Ki=13000nM
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:2zfp, PDBe:2zfp, PDBj:2zfp
PDBsum2zfp
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]