Research workbench
P53 cancer mutant Y220S in complex with small-molecule stabilizer PK9323
Analyse P53 cancer mutant Y220S in complex with small-molecule stabilizer PK9323 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SI4
- 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
- LEK, ZN
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 8% 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 | 196 | 7% helix, 33% strand | P04637 |
Ligands and binding sites
- LEK · 1-[9-ethyl-7-(1,3-thiazol-4-yl)carbazol-3-yl]-~{N}-methyl-methanamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 286 | 0.60 | 0.79 | 31 | empty |
| 2 | 78 | 0.44 | 0.80 | 19 | LEK |
| 3 | 69 | 0.42 | 0.80 | 17 | LEK |
| 4 | 126 | 0.41 | 0.75 | 20 | empty |
| 5 | 87 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SI4 · p53 cancer mutant Y220S in complex with small-molecule stabilizer PK9323 · 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 6SI4 · PDBe 6SI4 · UniProt P04637
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