MolNFT v1 · #135553 · protein
BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA
5U2F · Bromodomain-containing protein 4: “BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA”. X-ray diffraction, 1 ligand (82Y), 4 pockets (best druggability 0.51). MolNFT v1 #135553 on GenesisL1: 3D…
- PDB
- 5U2F
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 82Y
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 131 | 51% helix, 2% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 131 | 53% helix, 3% strand | O60885 |
Ligands and binding sites
- 82Y · N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide · ligand · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.51 | 0.82 | 19 | 82Y |
| 2 | 90 | 0.49 | 0.81 | 17 | 82Y |
| 3 | 100 | 0.42 | 0.78 | 20 | empty |
| 4 | 59 | 0.36 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5U2F · BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA · 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 0.98
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 5U2F · PDBe 5U2F · UniProt O60885
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