Research workbench
DYRK1A in complex with hg-8-60-1
Analyse DYRK1A in complex with hg-8-60-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIJ
- Type
- protein
- Length
- 1,359 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
- B5Z
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 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 | 342 | 35% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 36% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 338 | 38% helix, 18% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 339 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- B5Z · ~{N}-[5-[3-(2-morpholin-4-ylethylcarbamoylamino) phenyl]-[1,3]thiazolo[5,4-b]pyridin-2-yl]cyclopropanecarboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.85 | 0.87 | 101 | empty |
| 2 | 899 | 0.85 | 0.87 | 85 | empty |
| 3 | 955 | 0.79 | 0.81 | 83 | B5Z |
| 4 | 1026 | 0.77 | 0.79 | 88 | B5Z |
| 5 | 1129 | 0.77 | 0.79 | 96 | B5Z |
Interfaces
5 interfaces between chains.
- C–D · 1245 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1231 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 898 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 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 6EIJ · PDBe 6EIJ · UniProt Q13627
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