Research workbench
Crystal structure of human casein kinase I delta in complex with 4-(2, 5-dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H- imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide
Analyse Crystal structure of human casein kinase I delta in complex with 4-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MQV
- Type
- protein
- Length
- 1,721 residues
- Chains
- 6
- 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
- D5Q, PO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% 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 | 286 | 39% helix, 18% strand | P48730 |
| B, D, E | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 287 | 39% helix, 18% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 288 | 38% helix, 18% strand | P48730 |
| F | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 286 | 39% helix, 18% strand | P48730 |
Ligands and binding sites
- D5Q · 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide · ligand · 6 copies · chains A, E, B, C, D, F
- PO4 · Phosphate ion · ion · 21 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.79 | 0.82 | 81 | D5Q |
| 2 | 1194 | 0.77 | 0.79 | 103 | D5Q |
| 3 | 1154 | 0.77 | 0.79 | 90 | D5Q |
| 4 | 352 | 0.73 | 0.84 | 45 | empty |
| 5 | 1159 | 0.72 | 0.75 | 105 | empty |
Interfaces
12 interfaces between chains.
- D–F · 703 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 643 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 575 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5MQV · Crystal structure of human Casein Kinase I delta in complex with… · 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 5MQV · PDBe 5MQV · UniProt P48730
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