MolNFT v1 · #102582 · protein
Tetra-substituted imidazoles as a new class of inhibitors of the P53- MDM2 interaction
4OQ3 · E3 ubiquitin-protein ligase MDM2: “Tetra-substituted imidazoles as a new class of inhibitors of the P53- MDM2 interaction”. X-ray diffraction, 1 ligand (2V8), 7 pockets (best druggability 0.80). MolNFT v1 #102582 on GenesisL1: 3D…
- PDB
- 4OQ3
- Type
- protein
- Length
- 367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 2V8
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 93 | 44% helix, 17% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 91 | 44% helix, 14% strand | Q00987 |
| D | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 90 | 46% helix, 12% strand | Q00987 |
Ligands and binding sites
- 2V8 · 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.80 | 0.88 | 34 | 2V8 |
| 2 | 119 | 0.45 | 0.77 | 19 | 2V8 |
| 3 | 110 | 0.43 | 0.76 | 16 | 2V8 |
| 4 | 114 | 0.42 | 0.76 | 19 | 2V8 |
| 5 | 69 | 0.34 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 581 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 345 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OQ3 · Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction · the same entry in another collection · chain A against A, TM-score 1.00
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 Q00987
- Elsewhere: RCSB PDB 4OQ3 · PDBe 4OQ3 · UniProt Q00987
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