MolNFT v1 · #171439 · protein
Crystal structure of CLK3 in complex with macrocycle ODS2003128
6Z53 · Dual specificity protein kinase CLK3: “Crystal structure of CLK3 in complex with macrocycle ODS2003128”. X-ray diffraction, 2 ligands (Q7Z, PO4), 3 pockets (best druggability 0.69). MolNFT v1 #171439 on GenesisL1: 3D structure…
- PDB
- 6Z53
- Type
- protein
- Length
- 351 residues
- Chains
- 1
- 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
- Q7Z, PO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK3 (EC 2.7.12.1) | protein | 351 | 38% helix, 19% strand | P49761 |
Ligands and binding sites
- Q7Z · 6-(2-methoxyethoxy)-11,15-dimethyl-8-oxa-2,11,15,19,21, 23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.69 | 0.80 | 47 | Q7Z |
| 2 | 55 | 0.39 | 0.80 | 14 | EDO |
| 3 | 83 | 0.36 | 0.76 | 21 | empty |
Compared structures
- 6Z53 · Crystal structure of CLK3 in complex with macrocycle ODS2003128 · 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 A against A, TM-score 0.97
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 6Z53 · PDBe 6Z53 · UniProt P49761
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