Research workbench
CDPK1 from eimeria tenella in complex with inhibitor UW1521
Analyse CDPK1 from eimeria tenella in complex with inhibitor UW1521 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZB
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-like domain protein kinase
- UniProt
- Q3HNM4
- Ligands
- BK8, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-like domain protein kinase | protein | 466 | 50% helix, 13% strand | Q3HNM4 |
| B | Calmodulin-like domain protein kinase | protein | 464 | 50% helix, 13% strand | Q3HNM4 |
Ligands and binding sites
- BK8 · 4-(6-ethoxynaphthalen-2-yl)-6-(piperazin-1-ylmethyl)-2H-indazol-3-amine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.69 | 0.81 | 59 | empty |
| 2 | 270 | 0.69 | 0.84 | 32 | BK8 |
| 3 | 250 | 0.68 | 0.84 | 31 | BK8 |
| 4 | 75 | 0.66 | 0.92 | 18 | empty |
| 5 | 352 | 0.66 | 0.80 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZB · CDPK1 from Eimeria tenella in complex with inhibitor UW1521 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3HNM4
- Elsewhere: RCSB PDB 4YZB · PDBe 4YZB · UniProt Q3HNM4
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