MolNFT v1 · #149372 · protein
X-ray structure of CLK2-KD(136-496)/INDAZOLE1 at 2.39A
6FYK · Dual specificity protein kinase CLK2: “X-ray structure of CLK2-KD(136-496)/INDAZOLE1 at 2.39A”. X-ray diffraction, 1 ligand (EAZ), 8 pockets (best druggability 0.78). MolNFT v1 #149372 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6FYK
- Type
- protein
- Length
- 1,047 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase CLK2
- EC
- 2.7.12.1
- UniProt
- P49760
- Ligands
- EAZ
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dual specificity protein kinase CLK2 (EC 2.7.12.1) | protein | 349 | 38% helix, 20% strand | P49760 |
Ligands and binding sites
- EAZ · (2~{S})-4-methyl-1-[5-(3-methyl-2~{H}-indazol-5-yl) pyridin-3-yl]oxy-pentan-2-amine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.78 | 0.82 | 84 | empty |
| 2 | 423 | 0.65 | 0.78 | 46 | EAZ |
| 3 | 263 | 0.64 | 0.81 | 24 | EAZ |
| 4 | 289 | 0.64 | 0.80 | 28 | EAZ |
| 5 | 349 | 0.64 | 0.79 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 618 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 185 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FYK · X-Ray structure of CLK2-KD(136-496)/Indazole1 at 2.39A · the same entry in another collection · chain A against A, TM-score 1.00
- P49760 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK2 (P49760) · a predicted model of the same protein · chain C 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 P49760
- Elsewhere: RCSB PDB 6FYK · PDBe 6FYK · UniProt P49760
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