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Structure of the P53 core domain mutant Y220C bound to the small molecule PHIKAN7242
Analyse Structure of the P53 core domain mutant Y220C bound to the small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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