Structure of PDB 3vhi Chain B Binding Site BS01

Receptor Information

>3vhi Chain B (length=121) Species: 9031 (Gallus gallus)

KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGT
QNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSS
VNDIGDDWKATRVGINIFTRL

Ligand information

• Ligand ID: VHI
• InChI: InChI=1S/C18H22N2O5S/c21-15(22)9-5-4-8-14-16-13(11-26-14)20(17(23)19-16)18(24)25-10-12-6-2-1-3-7-12/h1-3,6-7,13-14,16H,4-5,8-11H2,(H,19,23)(H,21,22)/t13-,14-,16-/m0/s1
• InChIKey: BWNGWJMPVBQLHD-DZKIICNBSA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: c1ccc(cc1)COC(=O)N2C3CSC(C3NC2=O)CCCCC(=O)O
  OpenEye OEToolkits 1.7.2: c1ccc(cc1)COC(=O)N2[C@H]3CS[C@H]([C@H]3NC2=O)CCCCC(=O)O
  ACDLabs 12.01: O=C(O)CCCCC2SCC3N(C(=O)OCc1ccccc1)C(=O)NC23
  CACTVS 3.370: OC(=O)CCCC[C@@H]1SC[C@H]2[C@@H]1NC(=O)N2C(=O)OCc3ccccc3
  CACTVS 3.370: OC(=O)CCCC[CH]1SC[CH]2[CH]1NC(=O)N2C(=O)OCc3ccccc3
• Formula: C18 H22 N2 O5 S
• Name: 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid
• ZINC: ZINC000095920869
• PDB chain: 3vhi Chain B Residue 1124

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vhi Rational development of caged-biotin protein-labeling agents and some applications in live cells
• Resolution: 1.76 Å
• Binding residue (original residue number in PDB): N12 L14 S16 Y33 T35 V37 T38 W70 S75 T77 W97 I117 N118 I119
• Binding residue (residue number reindexed from 1): N10 L12 S14 Y31 T33 V35 T36 W68 S73 T75 W95 I115 N116 I117
• Annotation score: 1
• Binding affinity: MOAD: Ka=2300000M^-1

Gene Ontology

Molecular Function

• GO:0009374 biotin binding

Biological Process

• GO:0019731 antibacterial humoral response

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:3vhi, PDBe:3vhi, PDBj:3vhi
• PDBsum: 3vhi
• PubMed: 22035795
• UniProt: P02701|AVID_CHICK Avidin (Gene Name=AVD)