MolNFT v1 · #137033 · protein
Crystal structure of the first bromodomain of human brdt in complex with BI2536
5VBQ · Bromodomain testis-specific protein: “Crystal structure of the first bromodomain of human brdt in complex with BI2536”. X-ray diffraction, 2 ligands (R78, CL), 5 pockets (best druggability 0.74). MolNFT v1 #137033 on GenesisL1: 3D…
- 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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