4IHP | pdb_00004ihp

Crystal structure of TgCDPK1 with inhibitor bound

• PDB DOI: https://doi.org/10.2210/pdb4IHP/pdb

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


• Deposited: 2012-12-19 Released: 2014-01-15 
• Deposition Author(s): El Bakkouri, M., Tempel, W., Crandall, I.E., Massad, T., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kain, C.K., Shokat, K.M., Sibley, L.D., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.251 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of TgCDPK1 with inhibitor bound

El Bakkouri, M., Tempel, W., Crandall, I.E., Massad, T., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kain, C.K., Shokat, K.M., Sibley, L.D., Hui, R., Structural Genomics Consortium (SGC)

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: 57.65 kDa 
• Atom Count: 3,734 
• Modeled Residue Count: 454 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	507	Toxoplasma gondii	Mutation(s): 0  Gene Names: CDPK1, TGGT1_059880, TGVEG_042030 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FB	B [auth A]	1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C15 H16 Cl N5 O FOCSESRERLFAOP-UHFFFAOYSA-N
UNX	C [auth A], D [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
1FB	BindingDB:  4IHP	IC50: min: 9.99, max: 10 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.251 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.309	α = 90
b = 73.235	β = 90
c = 149.264	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): El Bakkouri, M., Tempel, W., Crandall, I.E., Massad, T., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kain, C.K., Shokat, K.M., Sibley, L.D., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations