MolNFT v1 · #126447 · protein
Crystal structure of BRD4 bromodomain 1 in complex with ligand 1
5M39 · Bromodomain-containing protein 4: “Crystal structure of BRD4 bromodomain 1 in complex with ligand 1”. X-ray diffraction, 1 ligand (7EA), 3 pockets (best druggability 0.56). MolNFT v1 #126447 on GenesisL1: 3D structure, binding sites…
- PDB
- 5M39
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 7EA
- Pockets
- 3 · best druggability 0.56
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 | 126 | 52% helix, 0% strand | O60885 |
Ligands and binding sites
- 7EA · 6-(3,4-dimethoxyphenyl)-3-methyl-[1,2,4]triazolo[4,3-b]pyridazine · 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 | 124 | 0.56 | 0.83 | 26 | 7EA |
| 2 | 267 | 0.54 | 0.76 | 31 | empty |
| 3 | 111 | 0.49 | 0.80 | 18 | 7EA |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5M39 · Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 1 · 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 5M39 · PDBe 5M39 · UniProt O60885
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