5W9E | pdb_00005w9e

Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186

PDB DOI: https://doi.org/10.2210/pdb5W9E/pdb

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

Deposited: 2017-06-23 Released: 2017-08-02
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.211 (Depositor), 0.220 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186

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.

To be published.

Macromolecule Content

Total Structure Weight: 55.56 kDa
Atom Count: 3,590
Modelled Residue Count: 451
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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(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 LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9YJ Query on 9YJ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-tert-butyl-3-[(3-chlorophenyl)sulfanyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine C₁₅ H₁₆ Cl N₅ S PNPUVQZAAVTLKS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9YJ	BindingDB: 5W9E	IC50: min: 13.8, max: 14 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.211 (Depositor), 0.220 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.997	α = 90
b = 72.802	β = 98.57
c = 64.595	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

El Bakkouri, M.

Rutaganaria, F.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.