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Second bromodomain (BD2) from candida albicans BDF1 bound to an imidazopyridine (compound 2)
Analyse Second bromodomain (BD2) from candida albicans BDF1 bound to an imidazopyridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N18
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing factor 1
- UniProt
- Q5A4W8
- Ligands
- 8HZ
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing factor 1 | protein | 106 | 68% helix, 0% strand | Q5A4W8 |
Ligands and binding sites
- 8HZ · 4-[8-methyl-3-[(4-methylphenyl)amino]imidazo[1,2-a]pyridin-2-yl]phenol · ligand · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.50 | 0.82 | 19 | GOL |
| 2 | 76 | 0.49 | 0.83 | 19 | 8HZ |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5N18 · Second Bromodomain (BD2) from Candida albicans Bdf1 bound to an imidazopyridine (compound… · 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 5N18 · PDBe 5N18 · UniProt Q5A4W8
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