Research workbench
Crystal structure of MDM2 (17-111) in complex with compound 29 (am- 8553)
Analyse Crystal structure of MDM2 (17-111) in complex with compound 29 (am- 8553) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ERF
- 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
- 0R3
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 92 | 45% helix, 17% strand | Q00987 |
| C, E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 93 | 45% helix, 18% strand | Q00987 |
Ligands and binding sites
- 0R3 · {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid · ligand · 3 copies · chains A, E, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.61 | 0.78 | 27 | 0R3 |
| 2 | 143 | 0.48 | 0.77 | 17 | 0R3 |
| 3 | 123 | 0.47 | 0.78 | 16 | 0R3 |
| 4 | 118 | 0.39 | 0.75 | 17 | empty |
| 5 | 62 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 575 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 320 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4ERF · crystal structure of MDM2 (17-111) in complex with compound 29 (AM-8553) · 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 4ERF · PDBe 4ERF · UniProt Q00987
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