MolNFT v1 · #172523 · protein
Structure of DYRK1A in complex with compound 6
7A52 · Dual specificity tyrosine-phosphorylation-regulated kinase…: “Structure of DYRK1A in complex with compound 6”. X-ray diffraction, 2 ligands (QYB, PO4), 6 pockets (best druggability 0.79). MolNFT v1 #172523 on GenesisL1: 3D…
- PDB
- 7A52
- Type
- protein
- Length
- 671 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
- QYB, PO4
- Pockets
- 6 · best druggability 0.79
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 | 338 | 36% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 36% helix, 18% strand | Q13627 |
Ligands and binding sites
- QYB · 3-phenyl-1H,4H,5H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.79 | 0.86 | 66 | QYB, PO4 |
| 2 | 471 | 0.75 | 0.84 | 49 | QYB, DMS |
| 3 | 82 | 0.45 | 0.80 | 19 | empty |
| 4 | 78 | 0.39 | 0.78 | 20 | empty |
| 5 | 65 | 0.38 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 24 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 7A52 · PDBe 7A52 · UniProt Q13627
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