Research workbench
Crystal structure of DCLK1-kd in complex with XMD8-85
Analyse Crystal structure of DCLK1-kd in complex with XMD8-85 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KX6
- Type
- protein
- Length
- 512 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
- X7Y
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 258 | 37% helix, 21% strand | O15075 |
| B | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 254 | 35% helix, 19% strand | O15075 |
Ligands and binding sites
- X7Y · 2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-B][1, 4]benzodiazepin-6-one · ligand · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.75 | 0.78 | 91 | X7Y |
| 2 | 192 | 0.46 | 0.74 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 201 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KX6 · Crystal structure of DCLK1-KD in complex with XMD8-85 · 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 0.94
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 7KX6 · PDBe 7KX6 · UniProt O15075
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