Research workbench
Crystal structure of the human bromodomain of EP300 bound to the inhibitor xdm-cbp
Analyse Crystal structure of the human bromodomain of EP300 bound to the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NU5
- Type
- protein
- Length
- 232 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
- 99E
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 116 | 68% helix, 0% strand | Q09472 |
Ligands and binding sites
- 99E · ~{N}-[[2,8-bis(oxidanyl)naphthalen-1-yl]methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.61 | 0.76 | 38 | EDO |
| 2 | 82 | 0.49 | 0.82 | 17 | 99E |
| 3 | 79 | 0.47 | 0.81 | 18 | 99E |
| 4 | 77 | 0.36 | 0.76 | 20 | empty |
| 5 | 81 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5NU5 · Crystal structure of the human bromodomain of EP300 bound to the inhibitor XDM-CBP · 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 5NU5 · PDBe 5NU5 · UniProt Q09472
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.