Structure of PDB 2vdm Chain B Binding Site BS01

Receptor Information

>2vdm Chain B (length=456) Species: 9606 (Homo sapiens)

GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCA
PESIEFPVSEARVLEDRPLSDKSQVTQVSPQRIALRLRPDDSKNFSIQVR
QVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGA
FVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNE
EVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTH
IALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKNIN
LIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKV
ELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRG
CPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTF
ECGVCR

Ligand information

• Ligand ID: AGG
• InChI: InChI=1S/C22H36N2O5S/c1-2-3-16-30(27,28)24-21(22(25)26)17-19-7-9-20(10-8-19)29-15-5-4-6-18-11-13-23-14-12-18/h7-10,18,21,23-24H,2-6,11-17H2,1H3,(H,25,26)/t21-/m0/s1
• InChIKey: COKMIXFXJJXBQG-NRFANRHFSA-N
• SMILES:
  CACTVS 3.341: CCCC[S](=O)(=O)N[CH](Cc1ccc(OCCCCC2CCNCC2)cc1)C(O)=O
  ACDLabs 10.04: O=S(=O)(NC(C(=O)O)Cc2ccc(OCCCCC1CCNCC1)cc2)CCCC
  OpenEye OEToolkits 1.5.0: CCCCS(=O)(=O)NC(Cc1ccc(cc1)OCCCCC2CCNCC2)C(=O)O
  OpenEye OEToolkits 1.5.0: CCCCS(=O)(=O)N[C@@H](Cc1ccc(cc1)OCCCCC2CCNCC2)C(=O)O
  CACTVS 3.341: CCCC[S](=O)(=O)N[C@@H](Cc1ccc(OCCCCC2CCNCC2)cc1)C(O)=O
• Formula: C22 H36 N2 O5 S
• Name: TIROFIBAN;
  N-(BUTYLSULFONYL)-O-[4-(4-PIPERIDINYL)BUTYL]-L-TYROSINE
• ChEMBL: CHEMBL916
• DrugBank: DB00775
• ZINC: ZINC000003806104
• PDB chain: 2vdm Chain B Residue 1462

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vdm Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): S121 Y122 S123 R214 N215 R216 D217 A218 E220
• Binding residue (residue number reindexed from 1): S116 Y117 S118 R209 N210 R211 D212 A213 E215
• Annotation score: 1
• Binding affinity: BindingDB: IC50=260000nM

External links

• PDB: RCSB:2vdm, PDBe:2vdm, PDBj:2vdm
• PDBsum: 2vdm
• PubMed: 18710925
• UniProt: P05106|ITB3_HUMAN Integrin beta-3 (Gene Name=ITGB3)