MolNFT v1 · #165803 · protein
BRD4-BD1 in complex with the cyclic peptide 3.1_2_ACK5TOA
6U72 · Bromodomain-containing protein 4: “BRD4-BD1 in complex with the cyclic peptide 3.1_2_ACK5TOA”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.57). MolNFT v1 #165803 on GenesisL1: 3D structure, binding sites…
- PDB
- 6U72
- Type
- protein
- Length
- 246 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; 3.1_2_ACK5TOA
- UniProt
- O60885
- Ligands
- ACE, NH2
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 127 | 54% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 105 | 62% helix, 0% strand | O60885 |
| C | 3.1_2_ACK5TOA | protein | 14 | 0% helix, 43% strand | — |
Ligands and binding sites
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 | 160 | 0.57 | 0.81 | 24 | empty |
| 2 | 116 | 0.50 | 0.80 | 21 | empty |
| 3 | 74 | 0.32 | 0.74 | 15 | empty |
| 4 | 55 | 0.26 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 355 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, acetylation).
Compared structures
- 6U72 · BRD4-BD1 in complex with the cyclic peptide 3.1_2_AcK5toA · 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 B against A, TM-score 0.98
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 6U72 · PDBe 6U72 · UniProt O60885
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