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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 57.65 kDa
Atom Count: 3,734
Modelled Residue Count: 454
Deposited Residue Count: 507
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	507	Toxoplasma gondii	Mutation(s): 0 Gene Names: CDPK1, TGGT1_059880, TGVEG_042030 EC: 2.7.11.17
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1FB Query on 1FB 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-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C₁₅ H₁₆ Cl N₅ O FOCSESRERLFAOP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

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), 0.250 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

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Crystal structure of TgCDPK1 with inhibitor bound

Crystal structure of TgCDPK1 with inhibitor bound

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4IHP | pdb_00004ihp