Research workbench
CK1D in complex with 1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4- YL]PYRIDIN-2-yl}-N-methylmethanamine ligand
Analyse CK1D in complex with 1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KB8
- Type
- protein
- Length
- 1,105 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, 2.7.11.26
- UniProt
- P48730
- Ligands
- 1QN, 1QO, SO4
- Pockets
- 11 · best druggability 0.76
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, 2.7.11.26) | protein | 265 | 40% helix, 20% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 285 | 39% helix, 18% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 277 | 42% helix, 19% strand | P48730 |
| D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 278 | 40% helix, 16% strand | P48730 |
Ligands and binding sites
- 1QN · 1-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}-N-methylmethanamine · ligand · 2 copies · chains A, C
- 1QO · N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.76 | 0.80 | 84 | SO4 |
| 2 | 588 | 0.75 | 0.82 | 74 | SO4 |
| 3 | 216 | 0.68 | 0.85 | 28 | 1QO |
| 4 | 214 | 0.63 | 0.83 | 35 | 1QN |
| 5 | 201 | 0.62 | 0.83 | 32 | 1QN |
Interfaces
4 interfaces between chains.
- C–D · 637 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 600 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 387 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4KB8 · CK1d in complex with 1-{4-[3-(4-FLUOROPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]PYRIDIN-2-YL}-N-MET… · 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 0.99
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 P48730
- Elsewhere: RCSB PDB 4KB8 · PDBe 4KB8 · UniProt P48730
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