Research workbench
Calcium-dependent protein kinase 1 from toxoplasma gondii (TGCDPK1) in complex with bumped kinase inhibitor rm-1-95
Analyse Calcium-dependent protein kinase 1 from toxoplasma gondii (TGCDPK1) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N51
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-domain protein kinase 1
- EC
- 2.7.11.17
- UniProt
- Q9BJF5
- Ligands
- BK3
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-domain protein kinase 1 (EC 2.7.11.17) | protein | 448 | 52% helix, 13% strand | Q9BJF5 |
Ligands and binding sites
- BK3 · 3-(naphthalen-1-ylmethyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.76 | 0.81 | 81 | BK3 |
| 2 | 62 | 0.68 | 0.95 | 16 | empty |
| 3 | 186 | 0.59 | 0.82 | 25 | empty |
| 4 | 134 | 0.45 | 0.77 | 27 | empty |
Compared structures
- 3N51 · Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with… · 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 Q9BJF5
- Elsewhere: RCSB PDB 3N51 · PDBe 3N51 · UniProt Q9BJF5
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