7T7S

Deposited: 2021-12-15 Released: 2022-02-02
Deposition Author(s): Reeve, S.M., Wang, S., Donald, B.R., Wright, D.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

(2022) PLoS Comput Biol 18: e1009855-e1009855

PubMed Abstract:
Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates (PLAs), next generation DHFR inhibitors, are much more resilient than TMP against this F98Y variant, yet this F98Y substitution still reduces efficacy of these agents. Surprisingly, differences in the enantiomeric configuration at the stereogenic center of PLAs influence the isomeric state of the NADPH cofactor. To understand the molecular basis of F98Y-mediated resistance and how PLAs' inhibition drives NADPH isomeric states, we used protein design algorithms in the osprey protein design software suite to analyze a comprehensive suite of structural, biophysical, biochemical, and computational data. Here, we present a model showing how F98Y SaDHFR exploits a different anomeric configuration of NADPH to evade certain PLAs' inhibition, while other PLAs remain unaffected by this resistance mechanism.

Organizational Affiliation

Department of Computer Science, Duke University, Durham, North Carolina, United States of America.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	157	Staphylococcus aureus	Mutation(s): 0 Gene Names: folA EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus) Explore P0A017 Go to UniProtKB: P0A017
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A017
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XNP (Subject of Investigation/LOI) Query on XNP Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X]	B [auth X]	Tricyclic NADPH C₂₁ H₃₀ N₇ O₁₇ P₃ AJKICLDTLPZSPE-MTKBYBFRSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
06U Query on 06U Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X]	C [auth X]	6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine C₂₂ H₂₃ N₅ O KEPLBUUTAQCZOE-AWEZNQCLSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X]	D [auth X]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History & Funding Information

Deposition Author(s):

Reeve, S.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI104841
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM078031
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118543