Research workbench
Crystal structure of DCLK1-kd in complex with nvp-TAE684
Analyse Crystal structure of DCLK1-kd in complex with nvp-TAE684 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JZN
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase DCLK1
- EC
- 2.7.11.1
- UniProt
- O15075
- Ligands
- GUI, SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 268 | 34% helix, 22% strand | O15075 |
| B | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 266 | 33% helix, 22% strand | O15075 |
Ligands and binding sites
- GUI · 5-chloro-N-[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N'-(2-propan-2-ylsulfonylphenyl)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
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 | 1026 | 0.84 | 0.85 | 102 | GUI, SO4 |
| 2 | 362 | 0.62 | 0.78 | 45 | empty |
| 3 | 150 | 0.50 | 0.78 | 18 | empty |
| 4 | 95 | 0.44 | 0.79 | 19 | empty |
| 5 | 65 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1718 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5JZN · Crystal structure of DCLK1-KD in complex with NVP-TAE684 · the same entry in another collection · chain A against A, TM-score 1.00
- O15075 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase DCLK1 (O15075) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 O15075
- Elsewhere: RCSB PDB 5JZN · PDBe 5JZN · UniProt O15075
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