MolNFT v1 · #161259 · protein
Structure of CLK1 with bound N-methyl-10-NITROPYRIDO[3,4-G]QUINAZOLIN- 2-amine
6Q8P · Dual specificity protein kinase CLK1: “Structure of CLK1 with bound N-methyl-10-NITROPYRIDO[3,4-G]QUINAZOLIN- 2-amine”. X-ray diffraction, 2 ligands (HQB, K), 7 pockets (best druggability 0.79). MolNFT v1 #161259 on GenesisL1: 3D…
- PDB
- 6Q8P
- Type
- protein
- Length
- 1,003 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
- HQB, K
- Pockets
- 7 · best druggability 0.79
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 | 336 | 38% helix, 19% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 333 | 38% helix, 18% strand | P49759 |
| C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 334 | 39% helix, 19% strand | P49759 |
Ligands and binding sites
- HQB · ~{N}-methyl-10-nitro-pyrido[3,4-g]quinazolin-2-amine · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.79 | 0.83 | 80 | HQB |
| 2 | 423 | 0.73 | 0.83 | 48 | HQB |
| 3 | 215 | 0.68 | 0.85 | 23 | HQB |
| 4 | 230 | 0.64 | 0.83 | 34 | empty |
| 5 | 157 | 0.53 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 612 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6Q8P · Structure of CLK1 with bound N-methyl-10-nitropyrido[3,4-g]quinazolin-2-amine · 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 A 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 6Q8P · PDBe 6Q8P · UniProt P49759
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