5F0A | pdb_00005f0a

CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb5F0A/pdb
Entry: 5F0A supersedes: 4WJC

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Plasmodium vivax Sal-1
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-11-27 Released: 2015-12-16
Deposition Author(s): Walker, J.R., Wernimont, A.K., He, H., Seitova, A., Loppnau, P., Sibley, L.D., Graslund, S., Hutchinson, A., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Hui, R., El Bakkouri, M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.242 (Depositor), 0.245 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND INHIBITOR

Walker, J.R., Wernimont, A.K., He, H., Seitova, A., Loppnau, P., Sibley, L.D., Graslund, S., Hutchinson, A., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Hui, R., El Bakkouri, M., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 97.04 kDa
Atom Count: 6,543
Modeled Residue Count: 811
Deposited Residue Count: 847
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase, putative	A	847	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVX_084705 EC: 2.7.11.12
UniProt
Find proteins for A5K0N4 (Plasmodium vivax (strain Salvador I)) Explore A5K0N4 Go to UniProtKB: A5K0N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K0N4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.242 (Depositor), 0.245 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.172	α = 90
b = 117.452	β = 94.55
c = 67.699	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-12-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 4WJC

Revision History (Full details and data files)

Version 1.0: 2015-12-16
Type: Initial release
Version 1.1: 2015-12-30
Changes: Other
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description