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Crystal structures of kinase domain of dap kinase in complex with small molecular inhibitors
Analyse Crystal structures of kinase domain of dap kinase in complex with small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WVX
- Type
- protein
- Length
- 275 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 1
- EC
- 2.7.1.37
- UniProt
- P53355
- Ligands
- BD4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.1.37) | protein | 275 | 37% helix, 20% strand | P53355 |
Ligands and binding sites
- BD4 · 6-(3-aminopropyl)-4,9-dimethylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.64 | 0.78 | 38 | BD4 |
| 2 | 73 | 0.34 | 0.76 | 18 | empty |
| 3 | 55 | 0.27 | 0.74 | 16 | empty |
Compared structures
- 1WVX · Crystal structures of kinase domain of DAP kinase in complex with small molecular… · the same entry in another collection · chain A against A, TM-score 1.00
- P53355 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 1 (P53355) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P53355
- Elsewhere: RCSB PDB 1WVX · PDBe 1WVX · UniProt P53355
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