Research workbench
Inhibitor of MDM2-P53 interaction
Analyse Inhibitor of MDM2-P53 interaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BJ0
- Type
- protein
- Length
- 187 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- TVH
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 93 | 47% helix, 15% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 94 | 48% helix, 16% strand | Q00987 |
Ligands and binding sites
- TVH · (3~{R})-4-chloranyl-3-(4-chlorophenyl)-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-2-[(4-nitrophenyl)methyl]isoindol-1-one · 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 | 119 | 0.47 | 0.78 | 19 | TVH |
| 2 | 90 | 0.39 | 0.76 | 20 | TVH |
Interfaces
1 interface between chains.
- A–B · 2275 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7BJ0 · Inhibitor of MDM2-p53 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 7BJ0 · PDBe 7BJ0 · UniProt Q00987
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