› 7u8z

X-ray diffraction
1.85Å resolution

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor

Released:
DOI: 10.2210/pdb7u8z/pdb
PDB entry 7u8z coloured by chain, front view.
PDB entry 7u8z coloured by chain, side view.
PDB entry 7u8z coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia.
Reßing N, Schliehe-Diecks J, Watson PR, Sönnichsen M, Cragin AD, Schöler A, Yang J, Schäker-Hübner L, Borkhardt A, Christianson DW, Bhatia S, Hansen FK
J Med Chem (2022)
PMID: 36351184

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UBP-type domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 364 amino acids
Theoretical weight: 40.29 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: F8W4B7 (Residues: 440-798; Coverage: 33%)
Gene name: hdac6
Sequence domains: Histone deacetylase domain

Ligands and Environments

7 bound ligands:
Ligand ACT 1 x ACT
Ligand M0I 4 x M0I
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand EDO 6 x EDO
Ligand GOL 1 x GOL
Ligand MLI 1 x MLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Spacegroup: P21
Unit cell:
a: 78.34Å b: 95.13Å c: 98.139Å
α: 90° β: 98.73° γ: 90°
R-values:
R R work R free
0.174 0.172 0.215
Expression system: Escherichia coli

Quick links

Citations

2 review citations

HDAC inhibitors enhance the anti-tumor effect of immunotherapies in hepatocellular carcinoma.
Shen et al. (2023)
1 more

1 mention without citation

Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia.
Reßing et al. (2022)