MolNFT v1 · #102066 · protein
Co-crystal structure of MDM2 (17-111) in complex with compound 25
4OAS · E3 ubiquitin-protein ligase MDM2: “Co-crystal structure of MDM2 (17-111) in complex with compound 25”. X-ray diffraction, 2 ligands (2SW, SO4), 5 pockets (best druggability 0.65). MolNFT v1 #102066 on GenesisL1: 3D structure…
- PDB
- 4OAS
- Type
- protein
- Length
- 278 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
- 2SW, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 93 | 44% helix, 17% strand | Q00987 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 92 | 49% helix, 17% strand | Q00987 |
Ligands and binding sites
- 2SW · [(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid · ligand · 3 copies · chains A, E, C
- SO4 · Sulfate ion · ion · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.65 | 0.79 | 25 | 2SW |
| 2 | 118 | 0.48 | 0.78 | 16 | 2SW |
| 3 | 127 | 0.46 | 0.77 | 18 | 2SW |
| 4 | 51 | 0.44 | 0.84 | 13 | empty |
| 5 | 105 | 0.39 | 0.76 | 18 | SO4 |
Interfaces
3 interfaces between chains.
- A–E · 513 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 299 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 222 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OAS · co-crystal structure of MDM2 (17-111) in complex with compound 25 · 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 4OAS · PDBe 4OAS · UniProt Q00987
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