Research workbench
Crystal structure of the first bromodomain of human brdt in complex with BI2536
Analyse Crystal structure of the first bromodomain of human brdt in complex with BI2536 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VBQ
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- R78, CL
- Pockets
- 5 · 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 | Bromodomain testis-specific protein | protein | 112 | 66% helix, 0% strand | Q58F21 |
Ligands and binding sites
- R78 · 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.74 | 0.87 | 35 | empty |
| 2 | 127 | 0.54 | 0.81 | 20 | R78, EDO |
| 3 | 130 | 0.52 | 0.80 | 22 | R78, EDO |
| 4 | 115 | 0.49 | 0.80 | 17 | EDO |
| 5 | 94 | 0.43 | 0.78 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5VBQ · Crystal structure of the first bromodomain of human brdt in complex with BI2536 · 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 B against A, TM-score 0.95
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 5VBQ · PDBe 5VBQ · UniProt Q58F21
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