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Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction
Analyse Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OQ3
- Type
- protein
- Length
- 367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- E3 ubiquitin-protein ligase Mdm2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 2V8
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.3 · 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
- Q00987 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (Q00987) · a predicted model of the same protein · chain A against A, TM-score 0.89
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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