MolNFT v1 · #113746 · protein
Structure of the P53 cancer mutant Y220C with bound small molecule PHIKAN7099
5AOK · Cellular tumor antigen P53: “Structure of the P53 cancer mutant Y220C with bound small molecule PHIKAN7099”. X-ray diffraction, 2 ligands (GOH, ZN), 4 pockets (best druggability 0.69). MolNFT v1 #113746 on GenesisL1: 3D structure…
- PDB
- 5AOK
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- GOH, ZN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 195 | 9% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- GOH · 5-[2-cyclopropyl-5-(1H-pyrrol-1-yl)-1,3-oxazol-4-yl]-1H-1,2,3,4-tetrazole · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
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 | 525 | 0.69 | 0.79 | 61 | GOL, GOH |
| 2 | 165 | 0.56 | 0.81 | 30 | GOL, GOH |
| 3 | 134 | 0.42 | 0.75 | 19 | empty |
| 4 | 118 | 0.39 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 288 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5AOK · Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan7099 · 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 5AOK · PDBe 5AOK · UniProt P04637
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