Research workbench
Crystal structure of human MDM2 with an imidazoline inhibitor
Analyse Crystal structure of human MDM2 with an imidazoline inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RV1
- Type
- protein
- Length
- 255 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-protein ligase E3 MDM2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- IMZ
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ubiquitin-protein ligase E3 MDM2 (EC 6.3.2.-) | protein | 85 | 44% helix, 20% strand | Q00987 |
Ligands and binding sites
- IMZ · Cis-[4,5-bis-(4-bromophenyl)-2-(2-ethoxy-4-methoxyphenyl)-4,5-dihydroimidazol-1-yl]-[4-(2-hydroxyethyl)piperazin-1-yl]methanone · ligand · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.79 | 0.80 | 45 | IMZ |
| 2 | 88 | 0.41 | 0.77 | 16 | IMZ |
Interfaces
3 interfaces between chains.
- A–B · 408 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 325 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RV1 · Crystal structure of human MDM2 with an imidazoline inhibitor · 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 1RV1 · PDBe 1RV1 · UniProt Q00987
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