MolNFT v1 · #113171 · protein
Structure of the P53 cancer Y220C bound to the stabilizing small molecule PHIKAN5211
5A7B · Cellular tumor antigen P53: “Structure of the P53 cancer Y220C bound to the stabilizing small molecule PHIKAN5211”. X-ray diffraction, 2 ligands (KMN, ZN), 6 pockets (best druggability 0.66). MolNFT v1 #113171 on GenesisL1: 3D…
- 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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