Structure of PDB 1ndj Chain D Binding Site BS01

Receptor Information

>1ndj Chain D (length=117) Species: 1895 (Streptomyces avidinii)

GITGTWYNQLGSTFIVTAGADGALTGTFESAVGNAESRYVLTGRYDSAPA
TDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTT
EANAWKSTLVGHDTFTK

Ligand information

• Ligand ID: BTN
• InChI: InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1
• InChIKey: YBJHBAHKTGYVGT-ZKWXMUAHSA-N
• SMILES:
  CACTVS 3.385: OC(=O)CCCC[CH]1SC[CH]2NC(=O)N[CH]12
  CACTVS 3.385: OC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
  ACDLabs 12.01: O=C1NC2C(SCC2N1)CCCCC(=O)O
  OpenEye OEToolkits 1.7.6: C1C2C(C(S1)CCCCC(=O)O)NC(=O)N2
  OpenEye OEToolkits 1.7.6: C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2
• Formula: C10 H16 N2 O3 S
• Name: BIOTIN
• ChEMBL: CHEMBL857
• DrugBank: DB00121
• ZINC: ZINC000035024346
• PDB chain: 1ndj Chain D Residue 5400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ndj Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.
• Resolution: 1.81 Å
• Binding residue (original residue number in PDB): N23 L25 S27 F43 S45 V47 G48 N49 W79 S88 T90 W108 D128
• Binding residue (residue number reindexed from 1): N8 L10 S12 F28 S30 V32 G33 N34 W64 S73 T75 W93 D113
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=12.16,Kd~0.69pM
  BindingDB: Kd=1.000000nM

Gene Ontology

Molecular Function

• GO:0009374 biotin binding

External links

• PDB: RCSB:1ndj, PDBe:1ndj, PDBj:1ndj
• PDBsum: 1ndj
• PubMed: 12925786
• UniProt: P22629|SAV_STRAV Streptavidin