MolNFT v1 · #111386 · protein
Crystal structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine
4YPD · Death-associated protein kinase 1: “Crystal structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine”. X-ray diffraction, 3 ligands (DKG, CL, SO4), 2 pockets (best druggability 0.71). MolNFT…
- PDB
- 4YPD
- Type
- protein
- Length
- 281 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
- DKG, CL, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 281 | 36% helix, 20% strand | P53355 |
Ligands and binding sites
- DKG · 4-methylpyridazine · ligand · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · 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 | 594 | 0.71 | 0.79 | 55 | CL, DKG |
| 2 | 86 | 0.39 | 0.77 | 17 | empty |
Compared structures
- 4YPD · Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment… · 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 0.94
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 4YPD · PDBe 4YPD · UniProt P53355
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