MolNFT v1 · #138112 · protein

Toxoplasma gondii CDPK1 in complex with inhibitor 3CIB-ppi

5W8R · Calmodulin-domain protein kinase 1: “Toxoplasma gondii CDPK1 in complex with inhibitor 3CIB-ppi”. X-ray diffraction, 2 ligands (9XV, CA), 5 pockets (best druggability 0.78). MolNFT v1 #138112 on GenesisL1: 3D structure, binding…

PDB: 5W8R
Type: protein
Length: 456 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calmodulin-domain protein kinase 1
UniProt: Q9BJF5
Ligands: 9XV, CA
Pockets: 5 · best druggability 0.78

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	protein	456	52% helix, 13% strand	Q9BJF5

Ligands and binding sites

9XV · 1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3, 4-d]pyrimidin-4-amine · ligand · chains A
CA · Calcium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	684	0.78	0.83	78	empty
2	375	0.78	0.87	56	9XV
3	65	0.70	0.96	15	empty
4	80	0.39	0.78	20	empty
5	60	0.36	0.79	16	empty

Compared structures

5W8R · Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI · 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 5W8R · PDBe 5W8R · UniProt Q9BJF5

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