MolNFT v1 · #84493 · protein
Structure of the P53 core domain mutant Y220C bound to the small molecule PHIKAN7242
3ZME · Cellular tumor antigen P53: “Structure of the P53 core domain mutant Y220C bound to the small molecule PHIKAN7242”. X-ray diffraction, 2 ligands (QC5, ZN), 5 pockets (best druggability 0.67). MolNFT v1 #84493 on GenesisL1: 3D…
- PDB
- 3ZME
- 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
- QC5, ZN
- Pockets
- 5 · best druggability 0.67
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
- QC5 · 2-(4-(4-fluorophenyl)-5-(1H-pyrrol-1-yl)-1H-pyrazol-1-yl)-N,N-dimethylethanamine · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.67 | 0.78 | 56 | empty |
| 2 | 142 | 0.54 | 0.81 | 30 | QC5 |
| 3 | 98 | 0.48 | 0.80 | 19 | QC5 |
| 4 | 136 | 0.42 | 0.75 | 19 | empty |
| 5 | 119 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 287 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ZME · Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242 · 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 3ZME · PDBe 3ZME · UniProt P04637
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