Research workbench
Discovery of spirohydantoins as selective, orally bioavailable inhibitors of P300/CBP histone acetyltransferases
Analyse Discovery of spirohydantoins as selective, orally bioavailable inhibitors of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJE
- Type
- protein
- Length
- 1,286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase P300
- EC
- 2.3.1.48, 2.3.1.-
- UniProt
- Q09472
- Ligands
- Y2P
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone acetyltransferase P300 (EC 2.3.1.48, 2.3.1.-) | protein | 319 | 42% helix, 21% strand | Q09472 |
| B, D | Histone acetyltransferase P300 (EC 2.3.1.48, 2.3.1.-) | protein | 324 | 42% helix, 20% strand | Q09472 |
Ligands and binding sites
- Y2P · 2-[4-[(3'R,4S)-3'-fluoro-1-[2-[(4-fluorophenyl)methyl-[(1S)-2,2,2-trifluoro-1-methyl-ethyl]amino]-2-oxo-ethyl]-2,5-dioxo-spiro[imidazolidine-4,1'-indane]-5'-yl]pyrazol-1-yl]-N-methyl-acetamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.79 | 0.81 | 88 | empty |
| 2 | 609 | 0.78 | 0.84 | 57 | Y2P |
| 3 | 342 | 0.76 | 0.87 | 36 | Y2P |
| 4 | 369 | 0.76 | 0.86 | 34 | Y2P |
| 5 | 523 | 0.74 | 0.82 | 52 | Y2P |
Interfaces
5 interfaces between chains.
- B–C · 783 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 781 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 452 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7LJE · Discovery of Spirohydantoins as Selective, Orally Bioavailable Inhibitors of p300/CBP… · the same entry in another collection · chain D against D, TM-score 1.00
- Q09472 · AlphaFold monomer V2.0 prediction for histone acetyltransferase P300 (Q09472) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q09472
- Elsewhere: RCSB PDB 7LJE · PDBe 7LJE · UniProt Q09472
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