Structure of PDB 3vhm Chain C Binding Site BS01

Receptor Information

>3vhm Chain C (length=123) Species: 9031 (Gallus gallus)

ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLH
GTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLR
SSVNDIGDDWKATRVGINIFTRL

Ligand information

• Ligand ID: NPK
• InChI: InChI=1S/C20H23N3O9S/c1-10(11-6-14-15(31-9-30-14)7-12(11)23(28)29)32-20(27)22-13-8-33-16(18(13)21-19(22)26)4-2-3-5-17(24)25/h6-7,10,13,16,18H,2-5,8-9H2,1H3,(H,21,26)(H,24,25)/t10-,13+,16-,18+/m1/s1
• InChIKey: MVOCLTWEOIJKEV-JTWAPGJUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C[C@H](c1cc2c(cc1[N+](=O)[O-])OCO2)OC(=O)N3[C@H]4CS[C@@H]([C@H]4NC3=O)CCCCC(=O)O
  OpenEye OEToolkits 1.7.6: CC(c1cc2c(cc1[N+](=O)[O-])OCO2)OC(=O)N3C4CSC(C4NC3=O)CCCCC(=O)O
  CACTVS 3.370: C[CH](OC(=O)N1[CH]2CS[CH](CCCCC(O)=O)[CH]2NC1=O)c3cc4OCOc4cc3[N+]([O-])=O
  CACTVS 3.370: C[C@@H](OC(=O)N1[C@H]2CS[C@H](CCCCC(O)=O)[C@H]2NC1=O)c3cc4OCOc4cc3[N+]([O-])=O
  ACDLabs 12.01: [O-][N+](=O)c1cc4OCOc4cc1C(OC(=O)N2C(=O)NC3C(SCC23)CCCCC(=O)O)C
• Formula: C20 H23 N3 O9 S
• Name: 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
• ZINC: ZINC000095920565
• PDB chain: 3vhm Chain A Residue 1124

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vhm Rational development of caged-biotin protein-labeling agents and some applications in live cells
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G107 W110
• Binding residue (residue number reindexed from 1): G107 W110
• Annotation score: 1
• Binding affinity: MOAD: Ka=15000M^-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:3vhm, PDBe:3vhm, PDBj:3vhm
• PDBsum: 3vhm
• PubMed: 22035795
• UniProt: P02701|AVID_CHICK Avidin (Gene Name=AVD)