Research workbench
Crystal structure of the first bromodomain of human BRD2 with the inhibitor GW841819X
Analyse Crystal structure of the first bromodomain of human BRD2 with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDW
- Type
- protein
- Length
- 319 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- WSH, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bromodomain-containing protein 2 | protein | 107 | 65% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 105 | 67% helix, 0% strand | P25440 |
Ligands and binding sites
- WSH · Benzyl [(4R)-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]carbamate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.66 | 0.79 | 49 | WSH |
| 2 | 119 | 0.51 | 0.80 | 18 | WSH |
| 3 | 104 | 0.49 | 0.80 | 20 | WSH |
| 4 | 78 | 0.40 | 0.79 | 18 | empty |
| 5 | 94 | 0.38 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1002 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YDW · Crystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GW841819X · the same entry in another collection · chain B against B, 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 2YDW · PDBe 2YDW · UniProt P25440
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