MolNFT v1 · #133749 · protein
Crystal structure of the first bromodomain of human BRD4 in complex with 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2- yl)-9H-carbazole-4-carboxamide
5S9P · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of human BRD4 in complex with…”. X-ray diffraction, 1 ligand (YW4), 6 pockets (best druggability 0.73). MolNFT v1 #133749 on GenesisL1: 3D structure…
- PDB
- 5S9P
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- YW4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Bromodomain-containing protein 4 | protein | 128 | 53% helix, 0% strand | O60885 |
Ligands and binding sites
- YW4 · 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide · ligand · 4 copies · chains A, D, B, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.73 | 0.80 | 53 | YW4 |
| 2 | 402 | 0.71 | 0.82 | 40 | YW4 |
| 3 | 419 | 0.62 | 0.77 | 48 | empty |
| 4 | 305 | 0.60 | 0.78 | 47 | empty |
| 5 | 123 | 0.54 | 0.81 | 20 | YW4 |
Interfaces
4 interfaces between chains.
- A–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 298 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 295 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 265 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5S9P · CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH… · the same entry in another collection · chain E against E, 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 0.97
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 5S9P · PDBe 5S9P · UniProt O60885
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