Research workbench
Crystal structure of CLK3 in complex with macrocycle ODS2004070
Analyse Crystal structure of CLK3 in complex with macrocycle ODS2004070 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z55
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase CLK3
- EC
- 2.7.12.1
- UniProt
- P49761
- Ligands
- PQ5, NA, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK3 (EC 2.7.12.1) | protein | 358 | 39% helix, 20% strand | P49761 |
| B | Dual specificity protein kinase CLK3 (EC 2.7.12.1) | protein | 357 | 39% helix, 20% strand | P49761 |
Ligands and binding sites
- PQ5 · 7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12, 6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 25 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 | 318 | 0.62 | 0.78 | 30 | PQ5 |
| 2 | 414 | 0.61 | 0.77 | 29 | EDO |
| 3 | 328 | 0.59 | 0.77 | 31 | PQ5 |
| 4 | 75 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6Z55 · Crystal structure of CLK3 in complex with macrocycle ODS2004070 · the same entry in another collection · chain A against A, TM-score 1.00
- P49761 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK3 (P49761) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P49761
- Elsewhere: RCSB PDB 6Z55 · PDBe 6Z55 · UniProt P49761
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