Research workbench
Crystal structure of human pcaf bromodomain in complex with compound BDOMB00091A (compound 14)
Analyse Crystal structure of human pcaf bromodomain in complex with compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FDZ
- Type
- protein
- Length
- 213 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
- 5X0
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 107 | 66% helix, 0% strand | Q92831 |
| B | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 106 | 66% helix, 0% strand | Q92831 |
Ligands and binding sites
- 5X0 · ~{N}-methyl-2-(oxan-4-yloxy)-5-(2-oxidanylidene-2-phenylazanyl-ethoxy)benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.62 | 0.77 | 48 | empty |
| 2 | 110 | 0.52 | 0.82 | 21 | 5X0 |
| 3 | 99 | 0.49 | 0.81 | 19 | 5X0 |
Interfaces
1 interface between chains.
- A–B · 709 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5FDZ · Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a… · 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 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 Q92831
- Elsewhere: RCSB PDB 5FDZ · PDBe 5FDZ · UniProt Q92831
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