› 3vzv

X-ray diffraction
2.8Å resolution

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Released:
DOI: 10.2210/pdb3vzv/pdb
PDB entry 3vzv coloured by chain, front view.
PDB entry 3vzv coloured by chain, side view.
PDB entry 3vzv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lead optimization of novel p53-MDM2 interaction inhibitors possessing dihydroimidazothiazole scaffold.
Miyazaki M, Naito H, Sugimoto Y, Kawato H, Okayama T, Shimizu H, Miyazaki M, Kitagawa M, Seki T, Fukutake S, Aonuma M, Soga T
Bioorg Med Chem Lett 23 728-32 (2013)
PMID: 23266121

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169499 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 87 amino acids
Theoretical weight: 10.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 25-109; Coverage: 17%)
  • Best match: Q00987-8 (Residues: 1-48)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

1 bound ligand:
Ligand VZV 2 x VZV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 58.255Å b: 66.076Å c: 80.419Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.248 0.284
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Small-molecule inhibitors of protein-protein interactions: progressing toward the reality.
Arkin et al. (2014)
2 more

5 mentions without citation

Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 Inhibitors) in clinical trials for cancer treatment.
Zhao et al. (2015)
4 more