MolNFT v1 · #106709 · protein
CK1D in complex with inhibitor
4TN6 · Casein kinase I isoform delta: “CK1D in complex with inhibitor”. X-ray diffraction, 2 ligands (PFO, SO4), 6 pockets (best druggability 0.64). MolNFT v1 #106709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TN6
- Type
- protein
- Length
- 577 residues
- Chains
- 2
- 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
- PFO, SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% 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 | 292 | 37% helix, 17% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 285 | 38% helix, 16% strand | P48730 |
Ligands and binding sites
- PFO · 4-{4-(4-fluorophenyl)-1-[1-(1,2-oxazol-3-ylmethyl)piperidin-4-yl]-1H-imidazol-5-yl}pyrimidin-2-amine · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.64 | 0.82 | 34 | empty |
| 2 | 315 | 0.63 | 0.79 | 34 | PFO |
| 3 | 183 | 0.61 | 0.82 | 24 | empty |
| 4 | 331 | 0.56 | 0.76 | 38 | empty |
| 5 | 180 | 0.56 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4TN6 · CK1d in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 4TN6 · PDBe 4TN6 · UniProt P48730
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