Research workbench
Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1
Analyse Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LPK
- Type
- protein
- Length
- 799 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase P300
- EC
- 2.3.1.48
- UniProt
- Q09472
- Ligands
- XDM, SO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 116 | 67% helix, 0% strand | Q09472 |
| B | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 112 | 68% helix, 0% strand | Q09472 |
| C | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 114 | 69% helix, 0% strand | Q09472 |
| D, F | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 115 | 69% helix, 0% strand | Q09472 |
| E | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 113 | 66% helix, 0% strand | Q09472 |
| G | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q09472 |
Ligands and binding sites
- XDM · ~{N}-[(3-chlorophenyl)methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide · ligand · 7 copies · chains A, C, B, D, F, E, G
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, E, F
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, C, D, B, E, F, G
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.86 | 0.87 | 137 | XDM, EDO |
| 2 | 550 | 0.79 | 0.85 | 54 | XDM |
| 3 | 73 | 0.60 | 0.89 | 21 | XDM |
| 4 | 244 | 0.55 | 0.77 | 27 | empty |
| 5 | 92 | 0.54 | 0.84 | 18 | empty |
Interfaces
11 interfaces between chains.
- E–G · 606 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 560 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 548 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5LPK · Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1 · the same entry in another collection · chain G against G, TM-score 1.00
- Q09472 · AlphaFold monomer V2.0 prediction for histone acetyltransferase P300 (Q09472) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 5LPK · PDBe 5LPK · UniProt Q09472
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