MolNFT v1 · #112278 · protein
Structure of MDM2 with low molecular weight inhibitor.
4ZGK · E3 ubiquitin-protein ligase MDM2: “Structure of MDM2 with low molecular weight inhibitor.”. X-ray diffraction, 1 ligand (4NX), 2 pockets (best druggability 0.49). MolNFT v1 #112278 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4ZGK
- Type
- protein
- Length
- 191 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
- Q00987
- Ligands
- 4NX
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 45% helix, 17% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 97 | 43% helix, 16% strand | Q00987 |
Ligands and binding sites
- 4NX · (5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-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 | 217 | 0.49 | 0.75 | 26 | 4NX |
| 2 | 152 | 0.47 | 0.76 | 20 | 4NX |
Interfaces
1 interface between chains.
- A–B · 397 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ZGK · Structure of Mdm2 with low molecular weight inhibitor. · 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 4ZGK · PDBe 4ZGK · UniProt Q00987
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