MolNFT v1 · #97365 · protein
CK1D in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H- pyrazol-4-YL]PYRIDIN-2-YL}MORPHOLINE inhibitor
4KBK · Casein kinase I isoform delta: “CK1D in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H- pyrazol-4-YL]PYRIDIN-2-YL}MORPHOLINE inhibitor”. X-ray diffraction, 2 ligands (1QG, SO4), 9 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 4KBK
- Type
- protein
- Length
- 1,133 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
- 1QG, SO4
- Pockets
- 9 · 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 | 283 | 41% helix, 19% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 289 | 39% helix, 19% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 280 | 41% helix, 18% strand | P48730 |
| D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 281 | 41% helix, 17% strand | P48730 |
Ligands and binding sites
- 1QG · (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}morpholine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.76 | 0.79 | 97 | SO4 |
| 2 | 677 | 0.74 | 0.80 | 81 | SO4 |
| 3 | 225 | 0.62 | 0.82 | 29 | 1QG |
| 4 | 185 | 0.60 | 0.82 | 30 | 1QG |
| 5 | 175 | 0.56 | 0.80 | 25 | 1QG |
Interfaces
5 interfaces between chains.
- A–B · 651 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 637 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 390 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KBK · CK1d in complex with (3S)-3-{4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]pyridin-2-yl}m… · 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 4KBK · PDBe 4KBK · UniProt P48730
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