MolNFT v1 · #187008 · protein
Crystal structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin- 4-yl)-1H-imidazol-5-yl]-N-(3,5-DIMETHYLPHENYL)PYRIMIDIN-2-amine
7RXR · Bromodomain-containing protein 4: “Crystal structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin…”. X-ray diffraction, 1 ligand (7ZB), 4 pockets (best druggability 0.58). MolNFT v1 #187008 on GenesisL1: 3D structure, binding…
- PDB
- 7RXR
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 7ZB
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 124 | 53% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 127 | 53% helix, 0% strand | O60885 |
Ligands and binding sites
- 7ZB · 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.58 | 0.78 | 40 | EDO |
| 2 | 115 | 0.54 | 0.82 | 18 | 7ZB |
| 3 | 114 | 0.52 | 0.81 | 19 | 7ZB |
| 4 | 106 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RXR · Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-y… · 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 0.99
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 7RXR · PDBe 7RXR · UniProt O60885
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