Research workbench
Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid
Analyse Co-crystal structure of MDM2 with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JWR
- Type
- protein
- Length
- 264 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- E3 ubiquitin-protein ligase Mdm2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 1MY
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.35 · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase Mdm2 (EC 6.3.2.-) | protein | 88 | 47% helix, 18% strand | Q00987 |
Ligands and binding sites
- 1MY · {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid · ligand · 3 copies · chains A, 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 | 260 | 0.63 | 0.81 | 34 | empty |
| 2 | 246 | 0.56 | 0.77 | 25 | 1MY |
| 3 | 114 | 0.47 | 0.78 | 16 | 1MY |
| 4 | 123 | 0.46 | 0.79 | 34 | empty |
| 5 | 104 | 0.45 | 0.78 | 16 | 1MY |
Interfaces
3 interfaces between chains.
- A–B · 593 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JWR · Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00987 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (Q00987) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 4JWR · PDBe 4JWR · UniProt Q00987
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