MolNFT v1 · #113056 · protein
DYRK1A in complex with hydroxy benzothiazole fragment
5A3X · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A in complex with hydroxy benzothiazole fragment”. X-ray diffraction, 1 ligand (QIV), 13 pockets (best druggability 0.85). MolNFT v1 #113056 on GenesisL1: 3D…
- PDB
- 5A3X
- Type
- protein
- Length
- 1,350 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
- QIV
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 37% 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 | 343 | 35% helix, 17% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 341 | 38% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 334 | 37% helix, 17% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 332 | 36% helix, 19% strand | Q13627 |
Ligands and binding sites
- QIV · N-(5-oxidanyl-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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.85 | 0.87 | 93 | empty |
| 2 | 1030 | 0.85 | 0.85 | 86 | empty |
| 3 | 742 | 0.80 | 0.84 | 89 | QIV |
| 4 | 678 | 0.80 | 0.84 | 81 | QIV |
| 5 | 571 | 0.78 | 0.84 | 65 | QIV |
Interfaces
6 interfaces between chains.
- A–B · 1253 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1248 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 974 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 959 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 3 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 0.98
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 5A3X · PDBe 5A3X · UniProt Q13627
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