MolNFT v1 · #190206 · protein
Crystal structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13157
7WMQ · Isoform 4 of bromodomain-containing protein 2: “Crystal structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13157”. X-ray diffraction, 1 ligand (JFL), 10 pockets (best druggability 0.59). MolNFT v1…
- PDB
- 7WMQ
- Type
- protein
- Length
- 441 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
- JFL
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform 4 of bromodomain-containing protein 2 | protein | 110 | 71% helix, 0% strand | P25440 |
| B | Isoform 4 of bromodomain-containing protein 2 | protein | 111 | 68% helix, 0% strand | P25440 |
| D | Isoform 4 of bromodomain-containing protein 2 | protein | 110 | 70% helix, 0% strand | P25440 |
Ligands and binding sites
- JFL · 2-(2-cyclobutyl-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
- FMT · Formic acid · additive · 15 copies · chains A, C, B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.59 | 0.76 | 39 | empty |
| 2 | 180 | 0.56 | 0.80 | 29 | empty |
| 3 | 311 | 0.54 | 0.75 | 36 | empty |
| 4 | 149 | 0.52 | 0.79 | 22 | JFL |
| 5 | 113 | 0.52 | 0.81 | 22 | JFL |
Interfaces
3 interfaces between chains.
- A–B · 835 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 792 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7WMQ · 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 D 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 P25440
- Elsewhere: RCSB PDB 7WMQ · PDBe 7WMQ · UniProt P25440
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