MolNFT v1 · #135550 · protein
BRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA
5U2C · Bromodomain-containing protein 4: “BRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA”. X-ray diffraction, 1 ligand (82Y), 3 pockets (best druggability 0.61). MolNFT v1 #135550 on GenesisL1: 3D…
- PDB
- 5U2C
- Type
- protein
- Length
- 231 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
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 120 | 62% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 111 | 63% helix, 0% 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.61 | 0.76 | 38 | empty |
| 2 | 129 | 0.51 | 0.80 | 19 | 82Y |
| 3 | 111 | 0.48 | 0.79 | 20 | 82Y |
Interfaces
1 interface between chains.
- A–B · 776 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5U2C · BRD4 second bromodomain (BD2) 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 B 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 5U2C · PDBe 5U2C · UniProt O60885
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