Research workbench
Crystal structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13120
Analyse Crystal structure of the second bromodomain of human BRD2 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WNA
- Type
- protein
- Length
- 648 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 4 of bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- JGR
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Isoform 4 of bromodomain-containing protein 2 | protein | 109 | 72% helix, 0% strand | P25440 |
| B | Isoform 4 of bromodomain-containing protein 2 | protein | 107 | 67% helix, 0% strand | P25440 |
| E | Isoform 4 of bromodomain-containing protein 2 | protein | 108 | 67% helix, 0% strand | P25440 |
| F | Isoform 4 of bromodomain-containing protein 2 | protein | 106 | 63% helix, 0% strand | P25440 |
Ligands and binding sites
- JGR · ~{N}-[4-(4-fluoranyl-2,6-dimethyl-phenoxy)-3-[2-[4-(2-hydroxyethyloxy)-3,5-dimethyl-phenyl]-5-methyl-4-oxidanylidene-furo[3,2-c]pyridin-7-yl]phenyl]ethanesulfonamide · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.82 | 0.83 | 87 | JGR |
| 2 | 635 | 0.78 | 0.83 | 61 | JGR, PEG |
| 3 | 575 | 0.77 | 0.83 | 55 | PEG, JGR |
| 4 | 416 | 0.66 | 0.79 | 58 | PEG, EDO |
| 5 | 196 | 0.53 | 0.78 | 26 | empty |
Interfaces
10 interfaces between chains.
- A–D · 666 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 421 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 417 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 401 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 347 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7WNA · Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor… · the same entry in another collection · chain E against E, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain B 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 7WNA · PDBe 7WNA · UniProt P25440
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