MolNFT v1 · #125993 · protein
Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1
5LPK · Histone acetyltransferase P300: “Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1”. X-ray diffraction, 2 ligands (XDM, SO4), 12 pockets (best druggability 0.86). MolNFT v1 #125993 on GenesisL1: 3D…
- 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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