› 5j7f

X-ray diffraction
2Å resolution

Structure of MDM2 with low molecular weight inhibitor with aliphatic linker.

Released:
DOI: 10.2210/pdb5j7f/pdb
PDB entry 5j7f coloured by chain, front view.
PDB entry 5j7f coloured by chain, side view.
PDB entry 5j7f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
1,4,5-Trisubstituted Imidazole-Based p53-MDM2/MDMX Antagonists with Aliphatic Linkers for Conjugation with Biological Carriers.
Twarda-Clapa A, Krzanik S, Kubica K, Guzik K, Labuzek B, Neochoritis CG, Khoury K, Kowalska K, Czub M, Dubin G, Dömling A, Skalniak L, Holak TA
J Med Chem 60 4234-4244 (2017)
PMID: 28482147

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169503 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 125 amino acids
Theoretical weight: 14.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 1-125; Coverage: 26%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

1 bound ligand:
Ligand 6GG 4 x 6GG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 37.758Å b: 174.75Å c: 37.81Å
α: 90° β: 93.48° γ: 90°
R-values:
R R work R free
0.186 0.183 0.242
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Small-molecule MDM2/X inhibitors and PROTAC degraders for cancer therapy: advances and perspectives.
Fang et al. (2020)
2 more