Research workbench
Crystal structure of DYRK2 in complex with eht 5372 (compound 1)
Analyse Crystal structure of DYRK2 in complex with eht 5372 (compound 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LXC
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 2
- EC
- 2.7.12.1
- UniProt
- Q92630
- Ligands
- 7AA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 2 (EC 2.7.12.1) | protein | 384 | 36% helix, 18% strand | Q92630 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 2 (EC 2.7.12.1) | protein | 386 | 37% helix, 18% strand | Q92630 |
Ligands and binding sites
- 7AA · methyl 9-[(2,4-dichlorophenyl)amino]-[1,3]thiazolo[5,4-f]quinazoline-2-carboximidate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
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 | 446 | 0.71 | 0.81 | 50 | 7AA, EDO |
| 2 | 224 | 0.63 | 0.82 | 27 | 7AA |
| 3 | 350 | 0.60 | 0.77 | 49 | EDO |
| 4 | 202 | 0.58 | 0.81 | 32 | empty |
| 5 | 297 | 0.54 | 0.75 | 37 | EDO |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
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 Q92630
- Elsewhere: RCSB PDB 5LXC · PDBe 5LXC · UniProt Q92630
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