Research workbench
Structure of a novel submicromolar MDM2 inhibitor
Analyse Structure of a novel submicromolar MDM2 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDN
- Type
- protein
- Length
- 94 residues
- Chains
- 1
- 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
- Y30, SO4
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 46% helix, 17% strand | Q00987 |
Ligands and binding sites
- Y30 · 3-{(1S)-2-(tert-butylamino)-1-[{4-[(4-chlorobenzyl)oxy]benzyl}(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.55 | 0.78 | 23 | Y30 |
Compared structures
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 4MDN · PDBe 4MDN · UniProt Q00987
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