MolNFT v1 · #40960 · protein
Crystal structure of human zip kinase in complex with a tetracyclic pyridone inhibitor (pyridone 6)
2J90 · Death-associated protein kinase 3: “Crystal structure of human zip kinase in complex with a tetracyclic pyridone inhibitor (pyridone 6)”. X-ray diffraction, 3 ligands (IZA, CL, PO4), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2J90
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 3
- EC
- 2.7.11.1
- UniProt
- O43293
- Ligands
- IZA, CL, PO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 265 | 40% helix, 21% strand | O43293 |
| B | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 264 | 37% helix, 19% strand | O43293 |
Ligands and binding sites
- IZA · 2-tert-butyl-9-fluoro-3,6-dihydro-7H-benz[h]-imidaz[4,5-f]isoquinoline-7-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 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 | 481 | 0.73 | 0.82 | 47 | IZA, CL, EDO |
| 2 | 654 | 0.70 | 0.78 | 46 | empty |
| 3 | 279 | 0.64 | 0.81 | 36 | IZA, CL, EDO |
| 4 | 128 | 0.41 | 0.75 | 20 | empty |
| 5 | 53 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2057 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 2J90 · Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O43293 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 3 (O43293) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O43293
- Elsewhere: RCSB PDB 2J90 · PDBe 2J90 · UniProt O43293
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