MolNFT v1 · #96734 · protein
The 2.5A crystal structure of humanized xenopus MDM2 with RO5316533 - a pyrrolidine MDM2 inhibitor
4JSC · E3 ubiquitin-protein ligase MDM2: “The 2.5A crystal structure of humanized xenopus MDM2 with RO5316533 - a pyrrolidine MDM2 inhibitor”. X-ray diffraction, 1 ligand (1OY), 2 pockets (best druggability 0.44). MolNFT v1 #96734 on…
- PDB
- 4JSC
- Type
- protein
- Length
- 166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 6.3.2.-
- UniProt
- P56273
- Ligands
- 1OY
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 45% helix, 14% strand | P56273 |
Ligands and binding sites
- 1OY · (3S,4R,5S)-3-(3-chloro-2-fluorophenyl)-4-(4-chloro-2-fluorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.44 | 0.77 | 17 | 1OY |
| 2 | 110 | 0.42 | 0.76 | 16 | 1OY |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4JSC · The 2.5A crystal structure of humanized Xenopus MDM2 with RO5316533 - a pyrrolidine MDM2… · the same entry in another collection · chain A against A, TM-score 1.00
- P56273 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (P56273) · a predicted model of the same protein · chain A against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P56273
- Elsewhere: RCSB PDB 4JSC · PDBe 4JSC · UniProt P56273
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