MolNFT v1 · #129801 · protein
Crystal structure of human BRD4(1) bromodomain in complex with DR46
5OVB · Bromodomain-containing protein 4: “Crystal structure of human BRD4(1) bromodomain in complex with DR46”. X-ray diffraction, 1 ligand (AY2), 5 pockets (best druggability 0.53). MolNFT v1 #129801 on GenesisL1: 3D structure, binding…
- PDB
- 5OVB
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- AY2
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 126 | 52% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 127 | 52% helix, 0% strand | O60885 |
Ligands and binding sites
- AY2 · ~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.53 | 0.77 | 30 | empty |
| 2 | 104 | 0.52 | 0.82 | 17 | AY2 |
| 3 | 88 | 0.50 | 0.82 | 17 | AY2 |
| 4 | 113 | 0.41 | 0.76 | 21 | empty |
| 5 | 78 | 0.39 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 304 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OVB · Crystal structure of human BRD4(1) bromodomain in complex with DR46 · 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 5OVB · PDBe 5OVB · UniProt O60885
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