4WG4 | pdb_00004wg4

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1613

• PDB DOI: https://doi.org/10.2210/pdb4WG4/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-17 Released: 2014-10-15 
• Deposition Author(s): Merritt, E.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1613

Merritt, E.A.

To be published.

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: 55.63 kDa 
• Atom Count: 3,751 
• Modeled Residue Count: 454 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	484	Toxoplasma gondii	Mutation(s): 0  Gene Names: CDPK1 EC: 2.7.11.17 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5  Go to UniProtKB:  Q9BJF5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UWB	B [auth A]	3-(7-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C23 H26 N6 O KMHCRQINFJTBPW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UWB	BindingDB:  4WG4	IC50: 19.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.69	α = 90
b = 73.18	β = 99.75
c = 66.77	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Merritt, E.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089441

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description