Research workbench
Identification and profiling of a selective and brain penetrant radioligand for in vivo target occupancy measurement of casein kinase 1 (CK1) inhibitors
Analyse Identification and profiling of a selective and brain penetrant radioligand for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W4W
- Type
- protein
- Length
- 1,153 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
- 9WG, SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 291 | 38% helix, 18% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 284 | 39% helix, 17% strand | P48730 |
| D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 287 | 39% helix, 20% strand | P48730 |
Ligands and binding sites
- 9WG · 4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-6-methyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.62 | 0.82 | 27 | 9WG |
| 2 | 219 | 0.62 | 0.82 | 31 | 9WG |
| 3 | 240 | 0.62 | 0.81 | 33 | 9WG |
| 4 | 220 | 0.61 | 0.81 | 36 | 9WG |
| 5 | 217 | 0.48 | 0.75 | 29 | SO4 |
Interfaces
1 interface between chains.
- B–D · 207 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5W4W · Identification and Profiling of a Selective and Brain Penetrant Radioligand for In Vivo… · 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 5W4W · PDBe 5W4W · UniProt P48730
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