MolNFT v1 · #150632 · protein
Crystal structure of human ckidelta with A86
6GZM · Casein kinase I isoform delta: “Crystal structure of human ckidelta with A86”. X-ray diffraction, 1 ligand (LCI), 7 pockets (best druggability 0.71). MolNFT v1 #150632 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GZM
- Type
- protein
- Length
- 586 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
- LCI
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 291 | 38% helix, 19% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 295 | 39% helix, 19% strand | P48730 |
Ligands and binding sites
- LCI · [4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.71 | 0.82 | 45 | LCI, GOL |
| 2 | 383 | 0.70 | 0.82 | 54 | LCI |
| 3 | 231 | 0.51 | 0.75 | 29 | empty |
| 4 | 63 | 0.42 | 0.81 | 12 | empty |
| 5 | 76 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1175 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6GZM · Crystal Structure of Human CKIdelta with A86 · 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 6GZM · PDBe 6GZM · UniProt P48730
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