MolNFT v1 · #178463 · protein
Crystal structure of the first bromodomain of BRD4 in complex with 16D10
7FH2 · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of BRD4 in complex with 16D10”. X-ray diffraction, 2 ligands (4JI, CL), 6 pockets (best druggability 0.73). MolNFT v1 #178463 on GenesisL1: 3D structure…
- PDB
- 7FH2
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 4JI, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 118 | 58% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 118 | 58% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 106 | 64% helix, 0% strand | O60885 |
| D | Bromodomain-containing protein 4 | protein | 104 | 63% helix, 0% strand | O60885 |
Ligands and binding sites
- 4JI · N-[2-[2-[(E)-3-(2,5-dimethoxyphenyl)prop-2-enoyl]-4,5-dimethoxy-phenyl]ethyl]ethanamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.73 | 0.79 | 64 | 4JI |
| 2 | 539 | 0.69 | 0.79 | 39 | empty |
| 3 | 112 | 0.57 | 0.84 | 25 | 4JI |
| 4 | 282 | 0.53 | 0.75 | 40 | CL |
| 5 | 104 | 0.47 | 0.80 | 18 | 4JI |
Interfaces
5 interfaces between chains.
- A–D · 454 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 321 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7FH2 · Crystal structure of the first bromodomain of BRD4 in complex with 16D10 · the same entry in another collection · chain D against D, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain D 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 7FH2 · PDBe 7FH2 · UniProt O60885
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