MolNFT v2 · #220509 · protein
DYRK1A complex with DYR530
8T2H · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A complex with DYR530”. X-ray diffraction at 1.85, 1 ligand (XIR), 7 pockets (best druggability 0.74). MolNFT v2 #220509 on GenesisL1: 3D structure, binding sites…
- PDB
- 8T2H
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 1A
- EC
- 2.7.11.23, 2.7.12.1
- UniProt
- Q13627
- Ligands
- XIR
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.11.23, 2.7.12.1) | protein | 339 | 37% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.11.23, 2.7.12.1) | protein | 342 | 35% helix, 18% strand | Q13627 |
Ligands and binding sites
- XIR · (4P)-4-{(3M)-3-[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]-2-methyl-3H-imidazo[4,5-b]pyridin-5-yl}pyridin-2-amine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.74 | 0.80 | 79 | XIR, GOL |
| 2 | 511 | 0.69 | 0.79 | 53 | XIR |
| 3 | 153 | 0.58 | 0.82 | 20 | empty |
| 4 | 161 | 0.45 | 0.75 | 27 | empty |
| 5 | 64 | 0.39 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1376 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
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 8T2H · PDBe 8T2H · UniProt Q13627
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