MolNFT v1 · #125995 · protein
Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM3D
5LPM · Histone acetyltransferase P300: “Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM3D”. X-ray diffraction, 1 ligand (71Y), 4 pockets (best druggability 0.67). MolNFT v1 #125995 on GenesisL1: 3D structure…
- PDB
- 5LPM
- 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
- 71Y
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone acetyltransferase P300 (EC 2.3.1.48) | protein | 116 | 65% helix, 0% strand | Q09472 |
Ligands and binding sites
- 71Y · ~{N}-[(1~{S},2~{S})-7-chloranyl-2-oxidanyl-1,2,3,4-tetrahydronaphthalen-1-yl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide · ligand · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.67 | 0.78 | 48 | 71Y, ACT |
| 2 | 72 | 0.46 | 0.82 | 17 | 71Y |
| 3 | 74 | 0.33 | 0.75 | 17 | ACT |
| 4 | 84 | 0.32 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LPM · Crystal structure of the bromodomain of human Ep300 bound to the inhibitor XDM3d · 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 0.98
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 5LPM · PDBe 5LPM · UniProt Q09472
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.