Research workbench
BRD4-BD1 in complex with the cyclic peptide 3.1_2
Analyse BRD4-BD1 in complex with the cyclic peptide 3.1_2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U74
- Type
- protein
- Length
- 493 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; Cyclic peptide 3.1_2
- UniProt
- O60885
- Ligands
- ACE, NH2
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 128 | 52% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 127 | 52% helix, 0% strand | O60885 |
| C, D | Bromodomain-containing protein 4 | protein | 105 | 62% helix, 0% strand | O60885 |
| E, F | Cyclic peptide 3.1_2 | protein | 14 | 0% helix, 29% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F
- NH2 · Amino group · ion · 2 copies · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.53 | 0.83 | 19 | empty |
| 2 | 110 | 0.51 | 0.81 | 19 | empty |
| 3 | 79 | 0.34 | 0.74 | 13 | empty |
| 4 | 74 | 0.32 | 0.74 | 21 | empty |
| 5 | 56 | 0.24 | 0.71 | 12 | empty |
Interfaces
7 interfaces between chains.
- A–E · 623 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 396 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 296 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent (acetylation, covalent ligand).
Compared structures
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 6U74 · PDBe 6U74 · UniProt O60885
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