Research workbench
Crystal structure of EP300 hat domain in complex with compound (+)-3
Analyse Crystal structure of EP300 hat domain in complex with compound (+)-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VHY
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase P300
- EC
- 2.3.1.48
- UniProt
- Q09472
- Ligands
- 6QI, ZN
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 437 | 35% helix, 23% strand | Q09472 |
| B | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 439 | 34% helix, 23% strand | Q09472 |
Ligands and binding sites
- 6QI · [(6R)-6-(1H-indazol-4-ylmethyl)-1,4-oxazepan-4-yl]-[1-(4-methoxyphenyl)cyclopentyl]methanone · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.82 | 0.83 | 77 | empty |
| 2 | 820 | 0.77 | 0.81 | 82 | 6QI |
| 3 | 306 | 0.71 | 0.84 | 35 | empty |
| 4 | 216 | 0.61 | 0.81 | 36 | empty |
| 5 | 206 | 0.60 | 0.81 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7VHY · Crystal structure of EP300 HAT domain in complex with compound (+)-3 · the same entry in another collection · chain A against A, 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 7VHY · PDBe 7VHY · UniProt Q09472
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