Research workbench
Crystal structure of DCLK1-kd in complex with DCLK1-in-1
Analyse Crystal structure of DCLK1-kd in complex with DCLK1-in-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KXW
- Type
- protein
- Length
- 506 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
- XBD
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 247 | 38% helix, 19% strand | O15075 |
| B | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 259 | 39% helix, 20% strand | O15075 |
Ligands and binding sites
- XBD · 2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.66 | 0.75 | 69 | XBD, PEG |
| 2 | 306 | 0.60 | 0.78 | 31 | XBD, PG4 |
Interfaces
1 interface between chains.
- A–B · 188 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7KXW · Crystal structure of DCLK1-KD in complex with DCLK1-IN-1 · 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 0.97
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 O15075
- Elsewhere: RCSB PDB 7KXW · PDBe 7KXW · UniProt O15075
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