MolNFT v1 · #166657 · protein
DYRK1A bound to a harmine derivative
6UWY · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A bound to a harmine derivative”. X-ray diffraction, 1 ligand (QKG), 19 pockets (best druggability 0.81). MolNFT v1 #166657 on GenesisL1: 3D structure, binding sites…
- PDB
- 6UWY
- Type
- protein
- Length
- 1,390 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
- QKG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 347 | 37% helix, 18% strand | Q13627 |
| B, D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 348 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- QKG · 4-(7-methoxy-1-methyl-9H-beta-carbolin-9-yl)butanamide · ligand · 4 copies · chains A, B, D, C
- PG4 · Tetraethylene glycol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.83 | 64 | PG4 |
| 2 | 750 | 0.73 | 0.79 | 78 | QKG, PG4 |
| 3 | 400 | 0.67 | 0.80 | 44 | QKG, PG4 |
| 4 | 220 | 0.65 | 0.83 | 24 | QKG |
| 5 | 228 | 0.63 | 0.82 | 26 | QKG |
Interfaces
3 interfaces between chains.
- B–D · 693 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 260 Ų buried · 2 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 6UWY · PDBe 6UWY · UniProt Q13627
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