MolNFT v1 · #190183 · protein
Crystal structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13153
7WLN · Isoform 4 of bromodomain-containing protein 2: “Crystal structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13153”. X-ray diffraction, 1 ligand (JFR), 9 pockets (best druggability 0.54). MolNFT v1…
- PDB
- 7WLN
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 4 of bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- JFR
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Isoform 4 of bromodomain-containing protein 2 | protein | 108 | 71% helix, 0% strand | P25440 |
| B, C | Isoform 4 of bromodomain-containing protein 2 | protein | 110 | 71% helix, 0% strand | P25440 |
Ligands and binding sites
- JFR · 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.54 | 0.74 | 36 | empty |
| 2 | 307 | 0.54 | 0.75 | 36 | empty |
| 3 | 193 | 0.53 | 0.78 | 29 | empty |
| 4 | 145 | 0.51 | 0.79 | 24 | JFR |
| 5 | 110 | 0.51 | 0.81 | 20 | JFR |
Interfaces
3 interfaces between chains.
- C–D · 805 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7WLN · Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor… · the same entry in another collection · chain D against D, 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 7WLN · PDBe 7WLN · UniProt P25440
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