Research workbench
Crystal structure of the first bromodomain (BD1) of human brdt bound to RO3280
Analyse Crystal structure of the first bromodomain (BD1) of human brdt bound to RO3280 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BJY
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- 79C
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of bromodomain testis-specific protein | protein | 108 | 65% helix, 0% strand | Q58F21 |
| B | Isoform 2 of bromodomain testis-specific protein | protein | 112 | 62% helix, 0% strand | Q58F21 |
Ligands and binding sites
- 79C · 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl) amino]-3-methoxy-N-(1-methylpiperidin-4-yl)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 | 269 | 0.58 | 0.78 | 36 | empty |
| 2 | 88 | 0.51 | 0.82 | 19 | 79C |
| 3 | 118 | 0.49 | 0.80 | 19 | 79C |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BJY · Crystal structure of the first bromodomain (BD1) of human BRDT bound to Ro3280 · the same entry in another collection · chain A against A, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · 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 Q58F21
- Elsewhere: RCSB PDB 7BJY · PDBe 7BJY · UniProt Q58F21
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