Structure of PDB 2zff Chain H Binding Site BS03

Receptor Information

>2zff Chain H (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G

Ligand information

• Ligand ID: 53U
• InChI: InChI=1S/C21H25N3O2/c22-18(14-16-8-3-1-4-9-16)21(26)24-13-7-12-19(24)20(25)23-15-17-10-5-2-6-11-17/h1-6,8-11,18-19H,7,12-15,22H2,(H,23,25)/t18-,19+/m1/s1
• InChIKey: MEPJWLFTTFHOQO-MOPGFXCFSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccccc3)N
  CACTVS 3.370: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccccc3
  ACDLabs 12.01: O=C(NCc1ccccc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
  OpenEye OEToolkits 1.7.0: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccccc3)N
  CACTVS 3.370: N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccccc3
• Formula: C21 H25 N3 O2
• Name: D-phenylalanyl-N-benzyl-L-prolinamide;
  (2S)-1-((2R)-2-amino-3-phenyl-propanoyl)-N-(phenylmethyl)pyrrolidine-2-carboxamide
• ChEMBL: CHEMBL116597
• DrugBank: DB07143
• ZINC: ZINC000053165085
• PDB chain: 2zff Chain H Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2zff Exploring Thrombin S1-pocket
• Resolution: 1.47 Å
• Binding residue (original residue number in PDB): Y60A W60D N98 A190 S195 V213 S214 W215 G216
• Binding residue (residue number reindexed from 1): Y47 W50 N95 A193 S198 V218 S219 W220 G221
• Annotation score: 1
• Binding affinity: BindingDB: Ki=4600nM

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

External links

• PDB: RCSB:2zff, PDBe:2zff, PDBj:2zff
• PDBsum: 2zff
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)