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)


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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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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase type 5
A, B
157Escherichia coliMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11731
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
560 (Subject of Investigation/LOI)
Query on 560

Download Ideal Coordinates CCD File 
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.42α = 90
b = 99.42β = 90
c = 43.406γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description