Structure of PDB 6tld Chain A Binding Site BS02

Receptor Information

>6tld Chain A (length=400) Species: 6183 (Schistosoma mansoni)

SVGIVYGDQYRQLCCSSPKFGDRYALVMDLINAYKLIPELSRVPPLQWDS
PSRMYEAVTAFHSTEYVDALKKLQMLHCEEKELTADDELLMDSFSLNYDC
PGFPSVFDYSLAAVQGSLAAASALICRHCEVVINWGGGWHHAKRSEASGF
CYLNDIVLAIHRLVSSQTRVLYVDLDLHHGDGVEEAFWYSPRVVTFSVHH
ASPGFFPGTGTWNKLPIFLNGAGRGRFSAFNLPLEEGINDLDWSNAIGPI
LDSLNIVIQPSYVVVQCGADCLATDPHRIFRLTNFYPSLSGYLYAIKKIL
SWKVPTLILGGGGYNFPDTARLWTRVTALTIEEVKGKKMTISPEIPEHSY
FSRYGPDFELDIDYFPDSIQKHHRRILEQLRNYADLNKLIYDYDQVYQLY

Ligand information

• Ligand ID: NK5
• InChI: InChI=1S/C9H8N4O2/c14-9(11-15)8-6-13(12-10-8)7-4-2-1-3-5-7/h1-6,15H,(H,11,14)
• InChIKey: ALZYWLPUOFGSEC-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)n2cc(nn2)C(=O)NO
  CACTVS 3.385: ONC(=O)c1cn(nn1)c2ccccc2
• Formula: C9 H8 N4 O2
• Name: ~{N}-oxidanyl-1-phenyl-1,2,3-triazole-4-carboxamide
• PDB chain: 6tld Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tld Structure-Based Design, Synthesis, and Biological Evaluation of Triazole-Based smHDAC8 Inhibitors.
• Resolution: 1.61 Å
• Binding residue (original residue number in PDB): D100 H142 G150 D186 H188 F216 Y341
• Binding residue (residue number reindexed from 1): D99 H141 G149 D176 H178 F206 Y314
• Annotation score: 1
• Binding affinity: MOAD: Kd=4.4uM
  PDBbind-CN: -logKd/Ki=5.35,IC50=4.44uM

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:6tld, PDBe:6tld, PDBj:6tld
• PDBsum: 6tld
• PubMed: 31816172
• UniProt: A5H660