Structure of PDB 3vgw Chain D Binding Site BS01

Receptor Information

>3vgw Chain D (length=121) Species: 9031 (Gallus gallus)

KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGT
QNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSS
VNDIGDDWKATRVGINIFTRL

Ligand information

• Ligand ID: NVZ
• InChI: InChI=1S/C12H18N2O4S/c1-7(15)14-8-6-19-9(11(8)13-12(14)18)4-2-3-5-10(16)17/h8-9,11H,2-6H2,1H3,(H,13,18)(H,16,17)/t8-,9-,11-/m0/s1
• InChIKey: LXKFOEIWWHPOIN-QXEWZRGKSA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: CC(=O)N1[C@H]2CS[C@H]([C@H]2NC1=O)CCCCC(=O)O
  OpenEye OEToolkits 1.7.2: CC(=O)N1C2CSC(C2NC1=O)CCCCC(=O)O
  CACTVS 3.370: CC(=O)N1[C@H]2CS[C@@H](CCCCC(O)=O)[C@H]2NC1=O
  CACTVS 3.370: CC(=O)N1[CH]2CS[CH](CCCCC(O)=O)[CH]2NC1=O
  ACDLabs 12.01: O=C(O)CCCCC1SCC2N(C(=O)C)C(=O)NC12
• Formula: C12 H18 N2 O4 S
• Name: 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
• ZINC: ZINC000095920950
• PDB chain: 3vgw Chain D Residue 1124

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vgw Rational development of caged-biotin protein-labeling agents and some applications in live cells
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): N12 L14 S16 Y33 T35 V37 T38 A39 W70 F72 S73 S75 T77 W97 N118
• Binding residue (residue number reindexed from 1): N10 L12 S14 Y31 T33 V35 T36 A37 W68 F70 S71 S73 T75 W95 N116
• Annotation score: 1
• Binding affinity: MOAD: Ka=200000M^-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:3vgw, PDBe:3vgw, PDBj:3vgw
• PDBsum: 3vgw
• PubMed: 22035795
• UniProt: P02701|AVID_CHICK Avidin (Gene Name=AVD)