Research workbench
Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (nmp) derivative 7B (1-methyl-4-(4-(piperidin-1-YLSULFONYL)PHENYL) pyrrolidin-2-one)
Analyse Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (nmp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VUC
- Type
- protein
- Length
- 126 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- RLS
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 126 | 54% helix, 0% strand | O60885 |
Ligands and binding sites
- RLS · (4R)-1-methyl-4-{4-[(piperidin-1-yl) sulfonyl]phenyl}pyrrolidin-2-one · ligand · 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 | 101 | 0.53 | 0.83 | 16 | RLS |
Compared structures
- 6VUC · Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 7b… · the same entry in another collection · chain A against A, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O60885
- Elsewhere: RCSB PDB 6VUC · PDBe 6VUC · UniProt O60885
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