7RGK

DfrA5 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)

PDB DOI: https://doi.org/10.2210/pdb7RGK/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-15 Released: 2022-05-25
Deposition Author(s): Lombardo, M.N., Wright, D.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.229
R-Value Work: 0.184
R-Value Observed: 0.186

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

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.

Krucinska, J., Lombardo, M.N., Erlandsen, H., Estrada, A., Si, D., Viswanathan, K., Wright, D.L.

(2022) Commun Biol 5: 459-459

PubMed: 35562546 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-022-03384-y
Primary Citation of Related Structures:
7MQP, 7MYL, 7MYM, 7NAE, 7R6G, 7REB, 7REG, 7RGJ, 7RGK, 7RGO

PubMed Abstract:
Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

Organizational Affiliation

Department of Pharmaceutical Sciences, University of Connecticut, 69N. Eagleville Rd., Storrs, CT, 06269, USA.

Macromolecule Content

Total Structure Weight: 37.8 kDa
Atom Count: 2,736
Modelled Residue Count: 314
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase type 5	A, B	157	Escherichia coli	Mutation(s): 0 Gene Names: dhfrV EC: 1.5.1.3
UniProt
Find proteins for P11731 (Escherichia coli) Explore P11731 Go to UniProtKB: P11731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11731
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
560 (Subject of Investigation/LOI) Query on 560 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine C₂₄ H₂₅ N₅ O₂ IIAMZXQFRCVQRC-AWEZNQCLSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]