Research workbench
DYRK1A in complex with chloro benzothiazole fragment
Analyse DYRK1A in complex with chloro benzothiazole fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A4Q
- Type
- protein
- Length
- 1,346 residues
- Chains
- 4
- 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
- Y3L
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 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 | 342 | 37% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 336 | 37% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 36% helix, 16% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 335 | 36% helix, 19% strand | Q13627 |
Ligands and binding sites
- Y3L · N-(5-chloranyl-1,3-benzothiazol-2-yl)ethanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.84 | 0.85 | 104 | empty |
| 2 | 1091 | 0.83 | 0.84 | 92 | empty |
| 3 | 1121 | 0.78 | 0.79 | 102 | Y3L |
| 4 | 661 | 0.77 | 0.82 | 73 | Y3L |
| 5 | 1101 | 0.77 | 0.79 | 92 | Y3L |
Interfaces
5 interfaces between chains.
- C–D · 1264 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1250 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 909 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).
Compared structures
- Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain A 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 Q13627
- Elsewhere: RCSB PDB 5A4Q · PDBe 5A4Q · UniProt Q13627
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