MolNFT v1 · #123030 · protein
Structure of MDM2 with low molecular weight inhibitor with aliphatic linker.
5J7F · E3 ubiquitin-protein ligase MDM2: “Structure of MDM2 with low molecular weight inhibitor with aliphatic linker.”. X-ray diffraction, 1 ligand (6GG), 5 pockets (best druggability 0.81). MolNFT v1 #123030 on GenesisL1: 3D structure…
- PDB
- 5J7F
- Type
- protein
- Length
- 404 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
- 6GG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 101 | 42% helix, 16% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 103 | 39% helix, 13% strand | Q00987 |
| D | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 99 | 41% helix, 15% strand | Q00987 |
Ligands and binding sites
- 6GG · 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.81 | 0.83 | 47 | 6GG |
| 2 | 824 | 0.80 | 0.82 | 48 | 6GG |
| 3 | 75 | 0.36 | 0.76 | 12 | empty |
| 4 | 80 | 0.34 | 0.75 | 17 | empty |
| 5 | 58 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 582 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5J7F · Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. · 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 5J7F · PDBe 5J7F · UniProt Q00987
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