Research workbench
Co-crystal structure of MDM2 with inhibitor compound 49
Analyse Co-crystal structure of MDM2 with inhibitor compound 49 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OGV
- Type
- protein
- Length
- 267 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
- 2U7
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 89 | 47% helix, 19% strand | Q00987 |
Ligands and binding sites
- 2U7 · [(2S,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid · ligand · 3 copies · chains A, C, B
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 | 252 | 0.57 | 0.78 | 22 | 2U7 |
| 2 | 161 | 0.48 | 0.77 | 28 | empty |
| 3 | 128 | 0.47 | 0.77 | 16 | 2U7 |
| 4 | 112 | 0.46 | 0.78 | 14 | 2U7 |
Interfaces
3 interfaces between chains.
- A–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 187 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4OGV · Co-Crystal Structure of MDM2 with Inhibitor Compound 49 · 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 4OGV · PDBe 4OGV · UniProt Q00987
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