MolNFT v1 · #118831 · protein
Crystal structure of human pcaf bromodomain in complex with compound BDOMB00091A (compound 14)
5FDZ · Histone acetyltransferase KAT2B: “Crystal structure of human pcaf bromodomain in complex with compound BDOMB00091A (compound 14)”. X-ray diffraction, 1 ligand (5X0), 3 pockets (best druggability 0.62). MolNFT v1 #118831 on…
- 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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