7SQM | pdb_00007sqm

Discovery and Preclinical Pharmacology of INE963, A Potent and Fast-Acting Blood-Stage Antimalarial with a High Barrier to Resistance and Potential for Single-Dose Cure in Uncomplicated Malaria

PDB DOI: https://doi.org/10.2210/pdb7SQM/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-11-05 Released: 2021-12-29
Deposition Author(s): Shu, W., Yokokawa, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Failure of artesunate-mefloquine combination therapy for uncompli-cated Plasmodium falciparum malaria in southern Cambodia.

Rogers, W.O., Wongsrichanalai, C.

(2009) Malar J 2009, 8, 10: 8-10

Macromolecule Content

Total Structure Weight: 40.92 kDa
Atom Count: 3,206
Modeled Residue Count: 346
Deposited Residue Count: 357
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase haspin	A	357	Homo sapiens	Mutation(s): 0 Gene Names: HASPIN, GSG2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens) Explore Q8TF76 Go to UniProtKB: Q8TF76
PHAROS: Q8TF76 GTEx: ENSG00000177602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TF76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A5G (Subject of Investigation/LOI) Query on A5G 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-[(4S)-5-(2,4-difluorophenyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl]-4-methylpiperidin-4-amine C₁₆ H₁₇ F₂ N₅ S ZGROGDMIGGHZAV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		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
A5G	BindingDB: 7SQM	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.026	α = 90
b = 77.045	β = 90
c = 86.308	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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.