Research workbench
Crystal structure of the human BRD2 BD1 bromodomain in complex with 9- (cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3- (3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide
Analyse Crystal structure of the human BRD2 BD1 bromodomain in complex with 9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5S9O
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- A0A140T9E9
- Ligands
- YW1
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 121 | 59% helix, 2% strand | A0A140T9E9 |
| B | Bromodomain-containing protein 2 | protein | 114 | 62% helix, 0% strand | A0A140T9E9 |
Ligands and binding sites
- YW1 · 9-(cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3-(3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.51 | 0.81 | 19 | YW1 |
| 2 | 125 | 0.50 | 0.80 | 20 | YW1 |
| 3 | 106 | 0.41 | 0.77 | 18 | EDO |
| 4 | 90 | 0.38 | 0.76 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 1129 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5S9O · CRYSTAL STRUCTURE OF THE HUMAN BRD2 BD1 BROMODOMAIN IN COMPLEX WITH… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A140T9E9
- Elsewhere: RCSB PDB 5S9O · PDBe 5S9O · UniProt A0A140T9E9
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