Research workbench
Crystal structure of MDM2 (17-111) in complex with compound 23
Analyse Crystal structure of MDM2 (17-111) in complex with compound 23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ERE
- Type
- protein
- Length
- 175 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
- 0R2, SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 85 | 44% helix, 18% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 90 | 47% helix, 17% strand | Q00987 |
Ligands and binding sites
- 0R2 · [(3R,5R,6S)-1-[(2S)-1-tert-butoxy-1-oxobutan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-2-oxopiperidin-3-yl]acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 109 | 0.46 | 0.78 | 17 | 0R2 |
| 2 | 103 | 0.43 | 0.77 | 15 | 0R2 |
Interfaces
1 interface between chains.
- A–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ERE · crystal structure of MDM2 (17-111) in complex with compound 23 · 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 4ERE · PDBe 4ERE · UniProt Q00987
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