Structure of PDB 6gxa Chain A Binding Site BS02

Receptor Information

>6gxa Chain A (length=399) Species: 6183 (Schistosoma mansoni)

SVGIVYGDQYRQLCCSSPKFGDRYALVMDLINAYKLIPELSRVPPLQWDS
PSRMYEAVTAFHSTEYVDALKKLQMLHCEEKELTADDELLMDSFSLNYDC
PGFPSVFDYSLAAVQGSLAAASALICRHCEVVINWGGGWHHAKRSEASGF
CYLNDIVLAIHRLVSSQTRVLYVDLDLHHGDGVEEAFWYSPRVVTFSVHH
ASPGFFPGTGTWNMLPIFLNGAGRGRFSAFNLPLEEGINDLDWSNAIGPI
LDSLNIVIQPSYVVVQCGADCLATDPHRIFRLTNFYPLSGYLYAIKKILS
WKVPTLILGGGGYNFPDTARLWTRVTALTIEEVKGKKMTISPEIPEHSYF
SRYGPDFELDIDYFPDSIQKHHRRILEQLRNYADLNKLIYDYDQVYQLY

Ligand information

• Ligand ID: TB8
• InChI: InChI=1S/C9H8ClNO2/c10-8-4-2-1-3-7(8)5-6-9(12)11-13/h1-6,13H,(H,11,12)/b6-5+
• InChIKey: HMGPSDPNANTYKH-AATRIKPKSA-N
• SMILES:
  CACTVS 3.385: ONC(=O)C=Cc1ccccc1Cl
  CACTVS 3.385: ONC(=O)\C=C\c1ccccc1Cl
  OpenEye OEToolkits 2.0.6: c1ccc(c(c1)C=CC(=O)NO)Cl
  OpenEye OEToolkits 2.0.6: c1ccc(c(c1)/C=C/C(=O)NO)Cl
• Formula: C9 H8 Cl N O2
• Name: (~{E})-3-(2-chlorophenyl)-~{N}-oxidanyl-prop-2-enamide
• ChEMBL: CHEMBL2032251
• PDB chain: 6gxa Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gxa Synthesis, Crystallization Studies, and in vitro Characterization of Cinnamic Acid Derivatives as SmHDAC8 Inhibitors for the Treatment of Schistosomiasis.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): K20 D100 H141 H142 D186 H188 F216 Y341
• Binding residue (residue number reindexed from 1): K19 D99 H140 H141 D176 H178 F206 Y313
• Annotation score: 1
• Binding affinity: MOAD: ic50=60nM
  PDBbind-CN: -logKd/Ki=4.22,IC50=60uM

Enzymatic activity

• Enzyme Commision number: 3.5.1.98: histone deacetylase.

Gene Ontology

Molecular Function

• GO:0004407 histone deacetylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0006338 chromatin remodeling

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:6gxa, PDBe:6gxa, PDBj:6gxa
• PDBsum: 6gxa
• PubMed: 29806110
• UniProt: A5H660