Research workbench
Structure of DYRK1A in complex with compound 7
Analyse Structure of DYRK1A in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A53
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- 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
- QYZ
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 335 | 36% helix, 17% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 334 | 36% helix, 18% strand | Q13627 |
Ligands and binding sites
- QYZ · (3~{E})-3-[(5-methylfuran-2-yl)methylidene]-1~{H}-indol-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.78 | 0.80 | 75 | empty |
| 2 | 394 | 0.65 | 0.79 | 40 | QYZ |
| 3 | 297 | 0.64 | 0.80 | 39 | QYZ |
| 4 | 78 | 0.41 | 0.79 | 19 | empty |
| 5 | 66 | 0.40 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 5 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 7A53 · PDBe 7A53 · UniProt Q13627
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