Structure of PDB 3x00 Chain D Binding Site BS01

Receptor Information

>3x00 Chain D (length=124) Species: 1895 (Streptomyces avidinii)

GSAEAGITGTWSDQLGDTFIVTAGADGALTGTYENAVGNAESRYVLTGRY
DSAPATDGSGTALGWTVAWKNNSKNAHSATTWSGQYVGGADAKINTQWLL
TSGTTNANAWKSTLVGHDTFTKVK

Ligand information

• Ligand ID: ZOF
• InChI: InChI=1S/C16H28N4O3S/c17-16-19-11-10-24-12(15(11)20-16)6-3-4-7-13(21)18-9-5-1-2-8-14(22)23/h11-12,15H,1-10H2,(H,18,21)(H,22,23)(H3,17,19,20)/t11-,12-,15-/m0/s1
• InChIKey: IAJKFHSLWUNBII-HUBLWGQQSA-N
• SMILES:
  CACTVS 3.385: OC(=O)CCCCCNC(=O)CCCC[CH]1SC[CH]2NC(=N)N[CH]12
  ACDLabs 12.01: O=C(O)CCCCCNC(=O)CCCCC1SCC2NC(=[N@H])NC12
  CACTVS 3.385: OC(=O)CCCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=N)N[C@H]12
  OpenEye OEToolkits 1.7.6: C1C2C(C(S1)CCCCC(=O)NCCCCCC(=O)O)NC(=N)N2
  OpenEye OEToolkits 1.7.6: [H]/N=C/1\N[C@H]2CS[C@H]([C@H]2N1)CCCCC(=O)NCCCCCC(=O)O
• Formula: C16 H28 N4 O3 S
• Name: 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid
• ZINC: ZINC000034054957
• PDB chain: 3x00 Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3x00 Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant.
• Resolution: 1.3 Å
• Binding residue (original residue number in PDB): D27 Y43 W79 S88 T90 W108 D128
• Binding residue (residue number reindexed from 1): D17 Y33 W69 S78 T80 W98 D118
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.08,Kd=0.83nM

Gene Ontology

Molecular Function

• GO:0009374 biotin binding

External links

• PDB: RCSB:3x00, PDBe:3x00, PDBj:3x00
• PDBsum: 3x00
• PubMed: 25560769
• UniProt: P22629|SAV_STRAV Streptavidin