› 4jv7

X-ray diffraction
2.2Å resolution

Co-crystal structure of MDM2 with inhibitor (2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one

Released:
DOI: 10.2210/pdb4jv7/pdb
PDB entry 4jv7 coloured by chain, front view.
PDB entry 4jv7 coloured by chain, side view.
PDB entry 4jv7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Rational design and binding mode duality of MDM2-p53 inhibitors.
Gonzalez-Lopez de Turiso F, Sun D, Rew Y, Bartberger MD, Beck HP, Canon J, Chen A, Chow D, Correll TL, Huang X, Julian LD, Kayser F, Lo MC, Long AM, McMinn D, Oliner JD, Osgood T, Powers JP, Saiki AY, Schneider S, Shaffer P, Xiao SH, Yakowec P, Yan X, Ye Q, Yu D, Zhao X, Zhou J, Medina JC, Olson SH
J Med Chem 56 4053-70 (2013)
PMID: 23597064

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 Chain: A
Molecule details ›
Chain: A
Length: 96 amino acids
Theoretical weight: 11.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 18-111; Coverage: 19%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: P41212
Unit cell:
a: 59.846Å b: 59.846Å c: 75.275Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.281
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Drugging the p53 pathway: understanding the route to clinical efficacy.
Khoo et al. (2014)
11 more

3 mentions without citation

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization.
Ustach et al. (2019)
2 more