MolNFT v1 · #153113 · protein
Crystal structure of the human GCN5 bromodomain in complex with compound (R,R)-36N
6J3P · Histone acetyltransferase KAT2A: “Crystal structure of the human GCN5 bromodomain in complex with compound (R,R)-36N”. X-ray diffraction, 1 ligand (B8O), 4 pockets (best druggability 0.54). MolNFT v1 #153113 on GenesisL1: 3D…
- PDB
- 6J3P
- Type
- protein
- Length
- 211 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase KAT2A
- EC
- 2.3.1.48, 2.3.1.-
- UniProt
- Q92830
- Ligands
- B8O
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2A (EC 2.3.1.48, 2.3.1.-) | protein | 108 | 68% helix, 0% strand | Q92830 |
| B | Histone acetyltransferase KAT2A (EC 2.3.1.48, 2.3.1.-) | protein | 103 | 65% helix, 0% strand | Q92830 |
Ligands and binding sites
- B8O · 2-{[(3R,5R)-5-(2,3-dihydro-1,4-benzodioxin-6-yl)-1-methylpiperidin-3-yl]amino}-3-methyl-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.54 | 0.82 | 24 | empty |
| 2 | 98 | 0.53 | 0.83 | 19 | B8O |
| 3 | 101 | 0.52 | 0.83 | 21 | B8O |
| 4 | 139 | 0.45 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 436 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6J3P · Crystal structure of the human GCN5 bromodomain in complex with compound (R,R)-36n · the same entry in another collection · chain A against A, TM-score 1.00
- Q92830 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT2A (Q92830) · a predicted model of the same protein · chain B 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 Q92830
- Elsewhere: RCSB PDB 6J3P · PDBe 6J3P · UniProt Q92830
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