Research workbench
Structure of the P53 cancer Y220C bound to the stabilizing small molecule PHIKAN5211
Analyse Structure of the P53 cancer Y220C bound to the stabilizing small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A7B
- 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
- KMN, ZN
- Pockets
- 6 · best druggability 0.66
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 | 196 | 10% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 197 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- KMN · 2-[[4-(diethylamino)piperidin-1-yl]methyl]-6-ethynyl-4-(3-phenoxyprop-1-ynyl)phenol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.66 | 0.77 | 57 | empty |
| 2 | 149 | 0.44 | 0.75 | 19 | empty |
| 3 | 57 | 0.42 | 0.82 | 18 | KMN |
| 4 | 65 | 0.41 | 0.80 | 19 | KMN |
| 5 | 122 | 0.39 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 273 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A7B · Structure of the p53 cancer Y220C bound to the stabilizing small molecule PhiKan5211 · 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 5A7B · PDBe 5A7B · UniProt P04637
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