Research workbench
X-ray crystal structure of 1,2,3-triazolobenzodiazepine in complex with BRD2(D2)
Analyse X-ray crystal structure of 1,2,3-triazolobenzodiazepine in complex with BRD2(D2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U6V
- Type
- protein
- Length
- 109 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- 7WY
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 109 | 69% helix, 0% strand | P25440 |
Ligands and binding sites
- 7WY · 5-[7-(4-chlorophenyl)-1-methyl-6,7-dihydro-5H-[1,2, 3]triazolo[1,5-d][1,4]benzodiazepin-9-yl]pyridin-2-amine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.52 | 0.81 | 19 | 7WY |
Compared structures
- 5U6V · X-ray crystal structure of 1,2,3-triazolobenzodiazepine in complex with BRD2(D2) · the same entry in another collection · chain A against A, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P25440
- Elsewhere: RCSB PDB 5U6V · PDBe 5U6V · UniProt P25440
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