MolNFT v1 · #55255 · protein
Crystal structure of the second bromodomain of human BRD4 with the inhibitor GW841819X
2YEM · Bromodomain-containing protein 4: “Crystal structure of the second bromodomain of human BRD4 with the inhibitor GW841819X”. X-ray diffraction, 1 ligand (WSH), 4 pockets (best druggability 0.52). MolNFT v1 #55255 on GenesisL1: 3D…
- PDB
- 2YEM
- Type
- protein
- Length
- 221 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- WSH
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 110 | 71% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 111 | 70% helix, 0% strand | O60885 |
Ligands and binding sites
- WSH · Benzyl [(4R)-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]carbamate · ligand · 2 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 | 191 | 0.52 | 0.78 | 20 | empty |
| 2 | 104 | 0.51 | 0.81 | 20 | WSH |
| 3 | 119 | 0.50 | 0.80 | 21 | WSH |
| 4 | 153 | 0.48 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2YEM · Crystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X · 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 2YEM · PDBe 2YEM · UniProt O60885
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