Structure of PDB 4i60 Chain A Binding Site BS01

Receptor Information
>4i60 Chain A (length=128) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARKCSLTGKWTNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLH
GTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLR
SSVNDIGDDWKATRVGINIFTRLRTQKE
Ligand information
Ligand IDB1R
InChIInChI=1S/C15H15N2O2S.C5H.Ru/c18-12(10-5-1-2-6-10)7-3-4-8-13-14-11(9-20-13)16-15(19)17-14;1-2-4-5-3-1;/h11,13-14H,3-4,7-9H2,(H2,16,17,19);1H;/t11-,13-,14-;;/m0../s1
InChIKeyAKXPPZSWSDFJHM-SLGHVJFOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1C2C(C(S1)CCCCC(=O)C34C5=C6[Ru]5378913(C6=C74)C4C8=C9C1=C34)NC(=O)N2
CACTVS 3.370[Ru]|1|2|3|4|5|6|7|8(|C9C|1=C|2C|3=C|49)|C%10=C|5C|6(C|7=C|8%10)C(=O)CCCC[CH]%11SC[CH]%12NC(=O)N[CH]%11%12
ACDLabs 12.01O=C1NC2C(SCC2N1)CCCCC(=O)C3%10C%12=C%11C6=C3[Ru]4564789%10C5=C4C9C8=C57
OpenEye OEToolkits 1.7.6C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)C34C5=C6[Ru]5378913(C6=C74)C4C8=C9C1=C34)NC(=O)N2
CACTVS 3.370[Ru]|1|2|3|4|5|6|7|8(|C9C|1=C|2C|3=C|49)|C%10=C|5C|6(C|7=C|8%10)C(=O)CCCC[C@@H]%11SC[C@@H]%12NC(=O)N[C@H]%11%12
FormulaC20 H16 N2 O2 Ru S
Name[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium;
biotinylruthenocene
ChEMBL
DrugBank
ZINC
PDB chain4i60 Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i60 Structural investigation of the interactions of biotinylruthenocene with avidin.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
L14 S16 Y33 T35 V37 T38 A39 T40 W70 S73 S75 T77 W97 S101 R114 N118
Binding residue
(residue number reindexed from 1)
L14 S16 Y33 T35 V37 T38 A39 T40 W70 S73 S75 T77 W97 S101 R114 N118
Annotation score1
Binding affinityMOAD: Kd=1.87uM
PDBbind-CN: -logKd/Ki=5.73,Kd=1.87uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0019731 antibacterial humoral response
Cellular Component
GO:0005576 extracellular region

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Molecular Function

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Cellular Component
External links
PDB RCSB:4i60, PDBe:4i60, PDBj:4i60
PDBsum4i60
PubMed23603015
UniProtP02701|AVID_CHICK Avidin (Gene Name=AVD)

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