› 6p5v

X-ray diffraction
1.4Å resolution

Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-methylbenzamide

Released:
DOI: 10.2210/pdb6p5v/pdb
PDB entry 6p5v coloured by chain, front view.
PDB entry 6p5v coloured by chain, side view.
PDB entry 6p5v coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation.
Kim HS, Hammill JT, Scott DC, Chen Y, Min J, Rector J, Singh B, Schulman BA, Guy RK
J Med Chem 62 8429-8442 (2019)
PMID: 31465221

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112949 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DCN1-like protein 1; Endolysin Chain: A
Molecule details ›
Chain: A
Length: 384 amino acids
Theoretical weight: 44.31 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: D9IEF7 (Residues: 1-164; Coverage: 100%)
  • Canonical: Q96GG9 (Residues: 62-259; Coverage: 76%)
Gene names: DCN1, DCUN1D1, DCUN1L1, RP42, SCCRO, T4Tp126, e
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand MPD 1 x MPD
Ligand O37 1 x O37
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 35.31Å b: 96.985Å c: 60.072Å
α: 90° β: 106.09° γ: 90°
R-values:
R R work R free
0.173 0.171 0.205
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Targeting neddylation E2s: a novel therapeutic strategy in cancer.
Zheng et al. (2021)
2 more

3 mentions without citation

Targeting cullin neddylation for cancer and fibrotic diseases.
He et al. (2023)
2 more