MolNFT v1 · #113298 · protein
Structure of the P53 cancer mutant Y220C with bound small molecule 7- ethyl-3-(piperidin-4-yl)-1H-indole
5AB9 · Cellular tumor antigen P53: “Structure of the P53 cancer mutant Y220C with bound small molecule 7- ethyl-3-(piperidin-4-yl)-1H-indole”. X-ray diffraction, 2 ligands (92O, ZN), 5 pockets (best druggability 0.65). MolNFT v1 #113298 on…
- PDB
- 5AB9
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- 92O, ZN
- Pockets
- 5 · best druggability 0.65
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 | 197 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- 92O · 7-ethyl-3-(piperidin-4-yl)-1H-indole · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.65 | 0.77 | 52 | empty |
| 2 | 66 | 0.46 | 0.83 | 19 | 92O |
| 3 | 65 | 0.43 | 0.81 | 18 | 92O |
| 4 | 145 | 0.43 | 0.75 | 20 | empty |
| 5 | 98 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 291 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5AB9 · Structure of the p53 cancer mutant Y220C with bound small molecule 7… · 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 5AB9 · PDBe 5AB9 · UniProt P04637
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