3NCG

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1

• PDB DOI: https://doi.org/10.2210/pdb3NCG/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Cryptosporidium parvum Iowa II
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-04 Released: 2010-07-21 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.305 
• R-Value Work: 0.250 
• R-Value Observed: 0.253 

Literature

Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii.

Murphy, R.C., Ojo, K.K., Larson, E.T., Castellanos-Gonzalez, A., Perera, B.G., Keyloun, K.R., Kim, J.E., Bhandari, J.G., Muller, N.R., Verlinde, C.L., White, A.C., Merritt, E.A., Van Voorhis, W.C., Maly, D.J.

(2010) ACS Med Chem Lett 1: 331-335

• PubMed: 21116453 
• DOI: https://doi.org/10.1021/ml100096t
• Primary Citation of Related Structures:  
  3MWU, 3N51, 3NCG


• PubMed Abstract: 
  

  The protozoans Cryptosporidium parvum and Toxoplasma gondii are parasites of major health concern to humans. Both parasites contain a group of calcium-dependent protein kinases (CDPKs), which are found in plants and ciliates but not in humans or fungi. Here we describe a series of potent inhibitors that target CDPK1 in C. parvum (CpCDPK1) and T. gondii (TgCDPK1). These inhibitors are highly selective for CpCDPK1 and TgCDPK1 over the mammalian kinases SRC and ABL. Furthermore, they are able to block an early stage of C. parvum invasion of HCT-8 host cells, which is similar to their effects on T. gondii invasion of human fibroblasts.

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Organizational Affiliation: 

Department of Chemistry, University of Washington.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.59 kDa 
• Atom Count: 3,530 
• Modelled Residue Count: 426 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	486	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: CDPK1, cgd3_920 EC: 2.7.11.17
UniProt
Find proteins for A3FQ16 (Cryptosporidium parvum (strain Iowa II)) Explore A3FQ16  Go to UniProtKB:  A3FQ16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BK1	E [auth A]	1-(1-methylethyl)-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C19 H19 N5 QFGDRGRJMYSRIW-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BK1	PDBBind:  3NCG	IC50: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.305 
• R-Value Work: 0.250 
• R-Value Observed: 0.253 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.991	α = 90
b = 55.968	β = 104.78
c = 81.972	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-06-20
  Changes: Data collection
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description