MolNFT v1 · #154624 · protein
Crystal structure of CLK1 in complex with cx-4945
6KHD · Dual specificity protein kinase CLK1: “Crystal structure of CLK1 in complex with cx-4945”. X-ray diffraction, 1 ligand (3NG), 10 pockets (best druggability 0.80). MolNFT v1 #154624 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KHD
- Type
- protein
- Length
- 979 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
- 3NG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 322 | 39% helix, 19% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 332 | 37% helix, 20% strand | P49759 |
| C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 325 | 38% helix, 19% strand | P49759 |
Ligands and binding sites
- 3NG · 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.80 | 0.83 | 97 | 3NG |
| 2 | 641 | 0.69 | 0.77 | 55 | 3NG |
| 3 | 424 | 0.68 | 0.80 | 48 | 3NG |
| 4 | 143 | 0.51 | 0.80 | 24 | empty |
| 5 | 65 | 0.46 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 392 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 18 Ų buried · 0 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 P49759
- Elsewhere: RCSB PDB 6KHD · PDBe 6KHD · UniProt P49759
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