Research workbench
Structure of the P53 cancer mutant Y220C with bound small molecule PHIKAN883
Analyse Structure of the P53 cancer mutant Y220C with bound small molecule PHIKAN883 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AOM
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- FY8, ZN
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 195 | 8% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 195 | 7% helix, 33% strand | P04637 |
Ligands and binding sites
- FY8 · N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.62 | 0.79 | 35 | GOL |
| 2 | 155 | 0.57 | 0.82 | 32 | FY8 |
| 3 | 81 | 0.52 | 0.85 | 20 | FY8 |
| 4 | 153 | 0.45 | 0.76 | 24 | empty |
| 5 | 153 | 0.43 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 294 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5AOM · Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan883 · 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 P04637
- Elsewhere: RCSB PDB 5AOM · PDBe 5AOM · UniProt P04637
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