MolNFT v1 · #149987 · protein
P53 cancer mutant Y220C in complex with small-molecule stabilizer PK9318
6GGB · Cellular tumor antigen P53: “P53 cancer mutant Y220C in complex with small-molecule stabilizer PK9318”. X-ray diffraction, 2 ligands (EXQ, ZN), 5 pockets (best druggability 0.69). MolNFT v1 #149987 on GenesisL1: 3D structure…
- PDB
- 6GGB
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- EXQ, ZN
- Pockets
- 5 · best druggability 0.69
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 | 198 | 9% helix, 33% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 198 | 8% helix, 33% strand | P04637 |
Ligands and binding sites
- EXQ · [9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.69 | 0.78 | 68 | EDO, EPE |
| 2 | 66 | 0.40 | 0.80 | 18 | EXQ |
| 3 | 66 | 0.40 | 0.80 | 17 | EXQ |
| 4 | 88 | 0.35 | 0.75 | 18 | empty |
| 5 | 50 | 0.35 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GGB · p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9318 · 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 6GGB · PDBe 6GGB · UniProt P04637
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