MolNFT v1 · #127594 · protein
First bromodomain (BD1) from candida albicans BDF1 bound to a dibenzothiazepinone (compound 3)
5N17 · Bromodomain-containing factor 1: “First bromodomain (BD1) from candida albicans BDF1 bound to a dibenzothiazepinone (compound 3)”. X-ray diffraction, 2 ligands (8FK, SO4), 4 pockets (best druggability 0.73). MolNFT v1 #127594 on…
- PDB
- 5N17
- Type
- protein
- Length
- 259 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing factor 1
- UniProt
- Q5A4W8
- Ligands
- 8FK, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing factor 1 | protein | 129 | 54% helix, 0% strand | Q5A4W8 |
| B | Bromodomain-containing factor 1 | protein | 130 | 56% helix, 0% strand | Q5A4W8 |
Ligands and binding sites
- 8FK · (2~{S})-~{N}-(5-methyl-6-oxidanylidene-benzo[b][1, 4]benzothiazepin-2-yl)oxolane-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
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 | 613 | 0.73 | 0.80 | 63 | empty |
| 2 | 86 | 0.48 | 0.81 | 17 | 8FK |
| 3 | 76 | 0.46 | 0.81 | 18 | 8FK |
| 4 | 68 | 0.42 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5N17 · First Bromodomain (BD1) from Candida albicans Bdf1 bound to a dibenzothiazepi (compound 3) · the same entry in another collection · chain A against A, TM-score 1.00
- Q5A4W8 · AlphaFold monomer V2.0 prediction for bromodomain-containing factor 1 (Q5A4W8) · 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 Q5A4W8
- Elsewhere: RCSB PDB 5N17 · PDBe 5N17 · UniProt Q5A4W8
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