Research workbench
Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the P53-MDM2 interaction with a distinct binding mode: HDM2 (MDM2) complexed with CPD5
Analyse Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZYC
- Type
- protein
- Length
- 255 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
- 4SS, SO4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 3 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 | 84 | 46% helix, 15% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 86 | 44% helix, 19% strand | Q00987 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 85 | 45% helix, 19% strand | Q00987 |
Ligands and binding sites
- 4SS · (S)-2-(2-((2H-tetrazol-5-yl)methoxy)-4-methylphenyl)-1-(4-chlorophenyl)-6,7-diethoxy-1,2-dihydroisoquinolin-3(4H)-one · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.82 | 54 | 4SS |
| 2 | 350 | 0.71 | 0.83 | 31 | 4SS |
Interfaces
2 interfaces between chains.
- A–B · 726 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ZYC · Discovery of dihydroisoquinoli derivatives as novel inhibitors of the p53-MDM2… · 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 4ZYC · PDBe 4ZYC · UniProt Q00987
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.