MolNFT v1 · #151399 · protein
Crystal structure of human casein kinase I delta in complex with a photoswitchable 2-azoimidazole-based inhibitor (compound 3)
6HMP · Casein kinase I isoform delta: “Crystal structure of human casein kinase I delta in complex with a photoswitchable 2-azoimidazole-based…”. X-ray diffraction, 2 ligands (GEW, PO4), 4 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 6HMP
- Type
- protein
- Length
- 564 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
- GEW, PO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% 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 | 286 | 41% helix, 18% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 278 | 38% helix, 19% strand | P48730 |
Ligands and binding sites
- GEW · 3-(2,5-dimethoxyphenyl)-~{N}-[4-[5-(4-fluorophenyl)-2-[(~{E})-(4-fluorophenyl)diazenyl]-3-methyl-imidazol-4-yl]pyridin-2-yl]propanamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.65 | 0.76 | 44 | empty |
| 2 | 207 | 0.64 | 0.83 | 33 | GEW |
| 3 | 239 | 0.61 | 0.81 | 31 | GEW |
| 4 | 54 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6HMP · Crystal structure of human Casein Kinase I delta in complex with a photoswitchable… · 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 6HMP · PDBe 6HMP · UniProt P48730
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