MolNFT v1 · #162548 · protein
Crystal structure of casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor
6RCH: “Crystal structure of casein kinase I isoform delta (CK1 delta) complexed with SR4133 inhibitor”. X-ray diffraction, 3 ligands (K0B, NA, SO4), 4 pockets (best druggability 0.63). MolNFT v1 #162548 on GenesisL1: 3D structure, binding…
- PDB
- 6RCH
- 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
- K0B, NA, SO4
- Pockets
- 4 · best druggability 0.63
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 | 293 | 40% helix, 19% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 293 | 40% helix, 19% strand | P48730 |
Ligands and binding sites
- K0B · ~{N}-[[4,5-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-naphthalen-2-yl-purin-6-amine · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 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 | 231 | 0.63 | 0.82 | 33 | K0B |
| 2 | 124 | 0.58 | 0.84 | 27 | empty |
| 3 | 328 | 0.54 | 0.74 | 42 | SO4 |
| 4 | 85 | 0.39 | 0.77 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 283 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6RCH · Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133… · the same entry in another collection · chain B against B, 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 6RCH · PDBe 6RCH · UniProt P48730
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