› 4j3e

X-ray diffraction
1.91Å resolution

The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a

Released:
DOI: 10.2210/pdb4j3e/pdb
PDB entry 4j3e coloured by chain, front view.
PDB entry 4j3e coloured by chain, side view.
PDB entry 4j3e coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Discovery of RG7112: A Small-Molecule MDM2 Inhibitor in Clinical Development.
Vu B, Wovkulich P, Pizzolato G, Lovey A, Ding Q, Jiang N, Liu JJ, Zhao C, Glenn K, Wen Y, Tovar C, Packman K, Vassilev L, Graves B
ACS Med Chem Lett 4 466-9 (2013)
PMID: 24900694

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-157449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chain: A
Molecule details ›
Chain: A
Length: 86 amino acids
Theoretical weight: 9.96 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P56273 (Residues: 20-105; Coverage: 18%)
Gene name: mdm2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

2 bound ligands:
Ligand NUT 1 x NUT
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: C2221
Unit cell:
a: 42.887Å b: 67.657Å c: 67.173Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.239
Expression system: Escherichia coli BL21

Quick links

Citations

80 review citations

Induced protein degradation: an emerging drug discovery paradigm.
Lai et al. (2017)
79 more

11 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)
10 more