Research workbench
Bromodomain of human BRPF1 with N-1,3-dimethyl-2-oxo-6-( piperidin-1-yl)-2,3-dihydro-1H-1,3-benzodiazol-5-yl-2- methoxybenzamide
Analyse Bromodomain of human BRPF1 with N-1,3-dimethyl-2-oxo-6-(… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UYE
- Type
- protein
- Length
- 218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin
- UniProt
- P55201
- Ligands
- 9F9
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peregrin | protein | 109 | 66% helix, 0% strand | P55201 |
Ligands and binding sites
- 9F9 · N-[1,3-dimethyl-2-oxo-6-(piperidin-1-yl)-2,3-dihydro-1H-benzimidazol-5-yl]-2-methoxybenzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, 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 | 580 | 0.74 | 0.81 | 56 | EDO |
| 2 | 82 | 0.51 | 0.83 | 18 | 9F9 |
| 3 | 79 | 0.48 | 0.82 | 18 | 9F9 |
Interfaces
1 interface between chains.
- A–B · 684 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 P55201
- Elsewhere: RCSB PDB 4UYE · PDBe 4UYE · UniProt P55201
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