8F82

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor MAM845


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Rational Exploration of 2,4-Diaminopyrimidines as DHFR Inhibitors Active against Mycobacterium abscessus and Mycobacterium avium , Two Emerging Human Pathogens.

Andrade Meirelles, M.Almeida, V.M.Sullivan, J.R.de Toledo, I.Dos Reis, C.V.Cunha, M.R.Zigweid, R.Shim, A.Sankaran, B.Woodward, E.L.Seibold, S.Liu, L.Mian, M.R.Battaile, K.P.Riley, J.Duncan, C.Simeons, F.R.C.Ferguson, L.Joji, H.Read, K.D.Lovell, S.Staker, B.L.Behr, M.A.Pilli, R.A.Counago, R.M.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01594
  • Primary Citation of Related Structures:  
    7K6C, 8F80, 8F81, 8F82, 8F83, 8F84, 8F85, 8TA0, 8TA1, 8TBR

  • PubMed Abstract: 

    Nontuberculous mycobacteria (NTM) are emerging human pathogens linked to severe pulmonary diseases. Current treatments involve the prolonged use of multiple drugs and are often ineffective. Bacterial dihydrofolate reductase (DHFR) is a key enzyme targeted by antibiotics in Gram-negative bacterial infections. However, existing DHFR inhibitors designed for Gram-negative bacteria often fail against mycobacterial DHFRs. Here, we detail the rational design of NTM DHFR inhibitors based on P218 , a malarial DHFR inhibitor. We identified compound 8 , a 2,4-diaminopyrimidine exhibiting improved pharmacological properties and activity against purified DHFR, and whole cell cultures of two predominant NTM species: Mycobacterium avium and Mycobacterium abscessus . This study underscores the potential of compound 8 as a promising candidate for the in vivo validation of DHFR as an effective treatment against NTM infections.


  • Organizational Affiliation

    Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, 13083-970-Campinas, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase173Mycobacterium ulcerans Agy99Mutation(s): 2 
Gene Names: dfrAMUL_2179
EC: 1.5.1.3
UniProt
Find proteins for A0PQG8 (Mycobacterium ulcerans (strain Agy99))
Explore A0PQG8 
Go to UniProtKB:  A0PQG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0PQG8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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

Download Ideal Coordinates CCD File 
B [auth A]3-{2-[3-({(6M)-2,4-diamino-6-[3-(trifluoromethyl)phenyl]pyrimidin-5-yl}oxy)propoxy]phenyl}propanoic acid
C23 H23 F3 N4 O4
DHSSDBBWRIMIDY-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.666α = 90
b = 66.739β = 90.48
c = 44.025γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
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 States75N93022C00036
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection
  • Version 1.2: 2024-11-06
    Changes: Database references, Structure summary