MolNFT v1 · #171435 · protein
Crystal structure of CLK1 in complex with macrocycle ODS2004070
6Z4Z · Dual specificity protein kinase CLK1: “Crystal structure of CLK1 in complex with macrocycle ODS2004070”. X-ray diffraction, 2 ligands (PQ5, PO4), 14 pockets (best druggability 0.72). MolNFT v1 #171435 on GenesisL1: 3D structure…
- PDB
- 6Z4Z
- Type
- protein
- Length
- 1,013 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase CLK1
- EC
- 2.7.12.1
- UniProt
- P49759
- Ligands
- PQ5, PO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 40% helix, 20% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 339 | 40% helix, 20% strand | P49759 |
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 · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.72 | 0.87 | 34 | PQ5 |
| 2 | 207 | 0.71 | 0.87 | 25 | PQ5 |
| 3 | 339 | 0.70 | 0.83 | 35 | PQ5 |
| 4 | 146 | 0.60 | 0.84 | 24 | empty |
| 5 | 150 | 0.59 | 0.84 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 430 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z4Z · Crystal structure of CLK1 in complex with macrocycle ODS2004070 · the same entry in another collection · chain A against A, TM-score 1.00
- P49759 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK1 (P49759) · a predicted model of the same protein · chain C 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 P49759
- Elsewhere: RCSB PDB 6Z4Z · PDBe 6Z4Z · UniProt P49759
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