MolNFT v1 · #107733 · protein
N-terminal bromodomain of human BRD4 with 7-(3,4-dimethoxyphenyl)-N- (1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-C-pyridine- 2- carboxamide
4UIX · Bromodomain-containing protein 4: “N-terminal bromodomain of human BRD4 with 7-(3,4-dimethoxyphenyl)-N…”. X-ray diffraction, 2 ligands (TVU, CA), 8 pockets (best druggability 0.56). MolNFT v1 #107733 on GenesisL1: 3D structure…
- PDB
- 4UIX
- Type
- protein
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- TVU, CA
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 126 | 53% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 126 | 56% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 115 | 57% helix, 0% strand | O60885 |
Ligands and binding sites
- TVU · N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.56 | 0.83 | 25 | TVU |
| 2 | 108 | 0.53 | 0.82 | 20 | TVU |
| 3 | 102 | 0.51 | 0.82 | 18 | TVU |
| 4 | 229 | 0.50 | 0.75 | 33 | EDO |
| 5 | 127 | 0.41 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 361 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 342 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4UIX · N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1-thian-4-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 B 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 4UIX · PDBe 4UIX · UniProt O60885
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