Research workbench
Crystal structure of CK1D with PF670462 from P1 crystal form
Analyse Crystal structure of CK1D with PF670462 from P1 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UYT
- Type
- protein
- Length
- 1,127 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase I isoform delta
- EC
- 2.7.11.1
- UniProt
- P48730
- Ligands
- 0CK, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase I isoform delta (EC 2.7.11.1) | protein | 287 | 40% helix, 18% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1) | protein | 286 | 39% helix, 16% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1) | protein | 286 | 39% helix, 18% strand | P48730 |
| D | Casein kinase I isoform delta (EC 2.7.11.1) | protein | 268 | 43% helix, 19% strand | P48730 |
Ligands and binding sites
- 0CK · 4-[1-cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.77 | 0.81 | 87 | SO4 |
| 2 | 602 | 0.71 | 0.79 | 56 | empty |
| 3 | 221 | 0.65 | 0.83 | 30 | 0CK |
| 4 | 182 | 0.64 | 0.84 | 29 | 0CK |
| 5 | 192 | 0.64 | 0.84 | 29 | 0CK |
Interfaces
4 interfaces between chains.
- A–D · 567 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 309 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 95 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3UYT · crystal structure of ck1d with PF670462 from P1 crystal form · the same entry in another collection · chain D against D, TM-score 1.00
- P48730 · AlphaFold monomer V2.0 prediction for casein kinase I isoform delta (P48730) · a predicted model of the same protein · chain C 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 P48730
- Elsewhere: RCSB PDB 3UYT · PDBe 3UYT · UniProt P48730
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