Research workbench
Crystal structure of human pcaf bromodomain in complex with compound SL1126 (compound 12)
Analyse Crystal structure of human pcaf bromodomain in complex with compound SL1126… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FE8
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase KAT2B
- EC
- 2.3.1.48
- UniProt
- Q92831
- Ligands
- 5WT
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 108 | 68% helix, 0% strand | Q92831 |
Ligands and binding sites
- 5WT · ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)ethanamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.68 | 0.78 | 37 | empty |
| 2 | 121 | 0.55 | 0.83 | 22 | 5WT |
| 3 | 107 | 0.54 | 0.83 | 18 | DMS |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5FE8 · Crystal structure of human PCAF bromodomain in complex with compound SL1126 (compound 12) · the same entry in another collection · chain A against A, TM-score 1.00
- Q92831 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT2B (Q92831) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q92831
- Elsewhere: RCSB PDB 5FE8 · PDBe 5FE8 · UniProt Q92831
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