Structure of PDB 2v3h Chain H Binding Site BS03

Receptor Information

>2v3h Chain H (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Ligand information

• Ligand ID: I25
• InChI: InChI=1S/C24H34N4O3/c1-6-16-11-18(13-20(12-16)31-15-24(2,3)14-28(4)5)21(23(29)30)27-19-9-7-17(8-10-19)22(25)26/h7-13,21,27H,6,14-15H2,1-5H3,(H3,25,26)(H,29,30)/t21-/m1/s1
• InChIKey: VVVFEPKRHINSIE-OAQYLSRUSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C(c1cc(OCC(C)(C)CN(C)C)cc(c1)CC)Nc2ccc(C(=[N@H])N)cc2
  OpenEye OEToolkits 1.5.0: [H]N=C(c1ccc(cc1)NC(c2cc(cc(c2)OCC(C)(C)CN(C)C)CC)C(=O)O)N
  OpenEye OEToolkits 1.5.0: [H]/N=C(/c1ccc(cc1)N[C@H](c2cc(cc(c2)OCC(C)(C)CN(C)C)CC)C(=O)O)\N
  CACTVS 3.341: CCc1cc(OCC(C)(C)CN(C)C)cc(c1)[CH](Nc2ccc(cc2)C(N)=N)C(O)=O
  CACTVS 3.341: CCc1cc(OCC(C)(C)CN(C)C)cc(c1)[C@@H](Nc2ccc(cc2)C(N)=N)C(O)=O
• Formula: C24 H34 N4 O3
• Name: (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID
• ZINC: ZINC000016052579
• PDB chain: 2v3h Chain H Residue 1246

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2v3h Fluorine in Pharmaceuticals: Looking Beyond Intuition.
• Resolution: 1.79 Å
• Binding residue (original residue number in PDB): Y60A W60D D189 A190 S195 W215 G216 G219
• Binding residue (residue number reindexed from 1): Y47 W50 D192 A193 S198 W220 G221 G223
• Annotation score: 1

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:2v3h, PDBe:2v3h, PDBj:2v3h
• PDBsum: 2v3h
• PubMed: 17901324
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)