MolNFT v1 · #107020 · protein
Crystal structure of DAPK1 kinase domain in complex with a small molecule inhibitor
4TXC · Death-associated protein kinase 1: “Crystal structure of DAPK1 kinase domain in complex with a small molecule inhibitor”. X-ray diffraction, 1 ligand (38G), 2 pockets (best druggability 0.65). MolNFT v1 #107020 on GenesisL1: 3D…
- PDB
- 4TXC
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- P53355
- Ligands
- 38G
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 276 | 34% helix, 19% strand | P53355 |
Ligands and binding sites
- 38G · 4-(3-{3-[(R)-{[2-(dimethylamino)ethyl]amino}(hydroxy)methyl]phenyl}imidazo[1,2-b]pyridazin-6-yl)-2-methoxyphenol · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.65 | 0.79 | 40 | 38G |
| 2 | 75 | 0.30 | 0.73 | 20 | EDO |
Compared structures
- 4TXC · Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor · 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 0.99
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 4TXC · PDBe 4TXC · UniProt P53355
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