Research workbench
Co-crystal structure of MDM2 with inhibitor compound 4
Analyse Co-crystal structure of MDM2 with inhibitor compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OBA
- Type
- protein
- Length
- 264 residues
- Chains
- 3
- 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
- 2TW
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 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
- 2TW · [(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.58 | 0.77 | 24 | 2TW |
| 2 | 116 | 0.49 | 0.79 | 16 | 2TW |
| 3 | 135 | 0.47 | 0.77 | 16 | 2TW |
| 4 | 64 | 0.30 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 583 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4OBA · Co-crystal structure of MDM2 with Inhibitor Compound 4 · 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 4OBA · PDBe 4OBA · UniProt Q00987
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