MolNFT v1 · #111572 · protein
CDPK1 from eimeria tenella in complex with inhibitor UW1354
4YUQ · Calmodulin-like domain protein kinase: “CDPK1 from eimeria tenella in complex with inhibitor UW1354”. X-ray diffraction, 2 ligands (KS1, CA), 20 pockets (best druggability 0.71). MolNFT v1 #111572 on GenesisL1: 3D structure, binding…
- PDB
- 4YUQ
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-like domain protein kinase
- UniProt
- Q3HNM4
- Ligands
- KS1, CA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-like domain protein kinase | protein | 462 | 48% helix, 13% strand | Q3HNM4 |
| B | Calmodulin-like domain protein kinase | protein | 462 | 48% helix, 13% strand | Q3HNM4 |
Ligands and binding sites
- KS1 · 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.71 | 0.98 | 24 | empty |
| 2 | 402 | 0.67 | 0.80 | 38 | empty |
| 3 | 70 | 0.67 | 0.93 | 12 | empty |
| 4 | 196 | 0.65 | 0.84 | 27 | KS1 |
| 5 | 341 | 0.64 | 0.80 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 148 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YUQ · CDPK1 from Eimeria tenella in complex with inhibitor UW1354 · 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 4YUQ · PDBe 4YUQ · UniProt Q3HNM4
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