MolNFT v1 · #82075 · protein
Structure of HDM2 with dimer inducing indolyl hydantoin ro-2443
3VBG · E3 ubiquitin-protein ligase MDM2: “Structure of HDM2 with dimer inducing indolyl hydantoin ro-2443”. X-ray diffraction, 1 ligand (03M), 4 pockets (best druggability 0.80). MolNFT v1 #82075 on GenesisL1: 3D structure, binding sites…
- PDB
- 3VBG
- Type
- protein
- Length
- 338 residues
- Chains
- 4
- 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
- 03M
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 84 | 45% helix, 11% strand | Q00987 |
| B, D | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 85 | 46% helix, 13% strand | Q00987 |
Ligands and binding sites
- 03M · (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.80 | 0.85 | 44 | 03M |
| 2 | 645 | 0.79 | 0.83 | 49 | 03M |
| 3 | 63 | 0.29 | 0.74 | 17 | empty |
| 4 | 55 | 0.28 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 550 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 491 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 348 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VBG · Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443 · 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 3VBG · PDBe 3VBG · UniProt Q00987
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