Research workbench
Structure of DYRK1A in complex with compound 34
Analyse Structure of DYRK1A in complex with compound 34 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A5N
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 1A
- EC
- 2.7.12.1
- UniProt
- Q13627
- Ligands
- R05, CL
- Pockets
- 7 · best druggability 0.76
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 1A (EC 2.7.12.1) | protein | 336 | 36% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 330 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- R05 · 5-(2-azanylpyridin-4-yl)-~{N}-[[2,6-bis(fluoranyl) phenyl]methyl]-2-methyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.76 | 0.84 | 48 | R05, CL |
| 2 | 337 | 0.74 | 0.85 | 44 | R05 |
| 3 | 75 | 0.49 | 0.84 | 15 | empty |
| 4 | 83 | 0.44 | 0.80 | 19 | empty |
| 5 | 80 | 0.40 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 774 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 Q13627
- Elsewhere: RCSB PDB 7A5N · PDBe 7A5N · UniProt Q13627
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