Research workbench
DYRK1A in complex with jwc-055
Analyse DYRK1A in complex with jwc-055 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIS
- Type
- protein
- Length
- 1,365 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
- B6N
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 35% 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 | 345 | 36% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 35% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 341 | 35% helix, 19% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 339 | 36% helix, 19% strand | Q13627 |
Ligands and binding sites
- B6N · 1-[4-fluoranyl-2-(trifluoromethyl)phenyl]-9-(1~{H}-pyrazol-4-yl)benzo[h][1,6]naphthyridin-2-one · 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 | 1124 | 0.88 | 0.88 | 156 | empty |
| 2 | 969 | 0.85 | 0.86 | 81 | empty |
| 3 | 643 | 0.80 | 0.85 | 68 | B6N |
| 4 | 1013 | 0.78 | 0.80 | 88 | B6N |
| 5 | 169 | 0.66 | 0.86 | 24 | B6N |
Interfaces
4 interfaces between chains.
- A–B · 1224 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1207 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 881 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 794 Ų buried · 11 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 6EIS · PDBe 6EIS · UniProt Q13627
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