MolNFT v1 · #117841 · protein
Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline inhibitor
5EK9 · Bromodomain-containing protein 2: “Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline inhibitor”. X-ray diffraction, 1 ligand (5P4), 4 pockets (best druggability 0.49). MolNFT v1 #117841…
- PDB
- 5EK9
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- 5P4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 2 | protein | 107 | 72% helix, 0% strand | P25440 |
Ligands and binding sites
- 5P4 · propan-2-yl ~{N}-[(2~{S},4~{R})-1-ethanoyl-6-(furan-2-yl)-2-methyl-3,4-dihydro-2~{H}-quinolin-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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.49 | 0.79 | 20 | 5P4 |
| 2 | 104 | 0.47 | 0.79 | 18 | 5P4 |
| 3 | 150 | 0.45 | 0.76 | 20 | empty |
| 4 | 141 | 0.43 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 734 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5EK9 · Crystal structure of the second bromodomain of human BRD2 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A 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 P25440
- Elsewhere: RCSB PDB 5EK9 · PDBe 5EK9 · UniProt P25440
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