Structure of PDB 4ydn Chain A Binding Site BS01

Receptor Information

>4ydn Chain A (length=116) Species: 9606 (Homo sapiens)

CPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLT
TEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAA
LLSPYSYSTTAVVTNP

Ligand information

• Ligand ID: 2WN
• InChI: InChI=1S/C14H7Cl2FN2O5S/c15-10-5-8(6-11(16)12(10)20)14-19-18-13(23-14)7-1-3-9(4-2-7)24-25(17,21)22/h1-6,20H
• InChIKey: RSJRYZBNJGGTGQ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Oc1c(Cl)cc(cc1Cl)c2oc(nn2)c3ccc(O[S](F)(=O)=O)cc3
  ACDLabs 12.01: FS(=O)(=O)Oc3ccc(c1nnc(o1)c2cc(Cl)c(O)c(Cl)c2)cc3
  OpenEye OEToolkits 1.7.6: c1cc(ccc1c2nnc(o2)c3cc(c(c(c3)Cl)O)Cl)OS(=O)(=O)F
• Formula: C14 H7 Cl2 F N2 O5 S
• Name: 4-[5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenyl sulfurofluoridate
• ZINC: ZINC000263620991
• PDB chain: 4ydn Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ydn A Fluorogenic Aryl Fluorosulfate for Intraorganellar Transthyretin Imaging in Living Cells and in Caenorhabditis elegans.
• Resolution: 1.35 Å
• Binding residue (original residue number in PDB): X15 A108 L110 S117 T118
• Binding residue (residue number reindexed from 1): X6 A99 L101 S108 T109
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.64,Kd=2.3nM

Gene Ontology

Molecular Function

• GO:0005179 hormone activity
• GO:0005515 protein binding
• GO:0042802 identical protein binding
• GO:0070324 thyroid hormone binding

Biological Process

• GO:0006144 purine nucleobase metabolic process
• GO:0007165 signal transduction

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0035578 azurophil granule lumen
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:4ydn, PDBe:4ydn, PDBj:4ydn
• PDBsum: 4ydn
• PubMed: 26051248
• UniProt: P02766|TTHY_HUMAN Transthyretin (Gene Name=TTR)