5W8R

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

PDB DOI: https://doi.org/10.2210/pdb5W8R/pdb

Classification: transferase/transferase inhibitor
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-22 Released: 2017-07-19
Deposition Author(s): El Bakkouri, M., Lovato, D., Loppnau, P., Lin, Y.H., Rutaganaria, F., Lopez, M.S., Shokat, L., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Sibley, D., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

El Bakkouri, M., Lovato, D., Loppnau, P., Lin, Y.H., Rutaganaria, F., Lopez, M.S., Shokat, L., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Sibley, D., Hui, R., Walker, J.R., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 55.58 kDa
Atom Count: 3,753
Modelled Residue Count: 456
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5 Go to UniProtKB: Q9BJF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BJF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9XV Query on 9XV Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine C₁₆ H₁₈ Cl N₅ VYDBKDXQXXHCLQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9XV	BindingDB: 5W8R	IC50: 3.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.024	α = 90
b = 72.944	β = 99.3
c = 65.546	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release
Version 1.1: 2017-11-15
Changes: Source and taxonomy
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5W8R

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)