MolNFT v1 · #111548 · protein
Crystal structure of DYRK1A with harmine-derivatized annh-75 inhibitor
4YU2 · Dual specificity tyrosine-phosphorylation-regulated kinase…: “Crystal structure of DYRK1A with harmine-derivatized annh-75 inhibitor”. X-ray diffraction, 2 ligands (4H5, SO4), 17 pockets (best druggability 0.81). MolNFT v1 #111548…
- PDB
- 4YU2
- Type
- protein
- Length
- 1,391 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
- 4H5, SO4
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 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 | 349 | 36% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 348 | 35% helix, 18% strand | Q13627 |
| C, D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 347 | 36% helix, 18% strand | Q13627 |
Ligands and binding sites
- 4H5 · (1-chloro-7-methoxy-9H-beta-carbolin-9-yl)acetonitrile · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains B, D, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.81 | 0.82 | 66 | empty |
| 2 | 742 | 0.73 | 0.79 | 74 | 4H5 |
| 3 | 363 | 0.68 | 0.81 | 40 | 4H5 |
| 4 | 414 | 0.68 | 0.80 | 49 | 4H5 |
| 5 | 363 | 0.67 | 0.81 | 40 | 4H5 |
Interfaces
3 interfaces between chains.
- B–D · 627 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 4 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 4YU2 · PDBe 4YU2 · UniProt Q13627
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