MolNFT v1 · #171119 · protein
CLK3 bound with beta-carboline kh-CARB13 (cpd 3)
6YU1 · Dual specificity protein kinase CLK3: “CLK3 bound with beta-carboline kh-CARB13 (cpd 3)”. X-ray diffraction, 2 ligands (KHC, PO4), 6 pockets (best druggability 0.63). MolNFT v1 #171119 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YU1
- Type
- protein
- Length
- 690 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
- KHC, PO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Dual specificity protein kinase CLK3 (EC 2.7.12.1) | protein | 340 | 39% helix, 19% strand | P49761 |
| c | Dual specificity protein kinase CLK3 (EC 2.7.12.1) | protein | 350 | 40% helix, 19% strand | P49761 |
Ligands and binding sites
- KHC · (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile · ligand · 2 copies · chains a, c
- PO4 · Phosphate ion · ion · 3 copies · chains a, c
- EDO · 1,2-ethanediol · additive · 22 copies · chains a, c
- PG4 · Tetraethylene glycol · additive · 2 copies · chains a, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.63 | 0.78 | 32 | KHC |
| 2 | 376 | 0.60 | 0.77 | 30 | EDO |
| 3 | 322 | 0.60 | 0.77 | 27 | KHC |
| 4 | 68 | 0.31 | 0.74 | 12 | empty |
| 5 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- a–c · 307 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 6YU1 · PDBe 6YU1 · UniProt P49761
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