7K6C | pdb_00007k6c

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 138.81 kDa 
  • Atom Count: 9,892 
  • Modeled Residue Count: 1,115 
  • Deposited Residue Count: 1,197 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrofolate reductase
A, B, C, D, E
A, B, C, D, E, F, G
171Mycobacteroides abscessus ATCC 19977Mutation(s): 2 
Gene Names: MAB_3090c
EC: 1.5.1.3
UniProt
Find proteins for B1MD46 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MD46 
Go to UniProtKB:  B1MD46
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MD46
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
(Subject of Investigation/LOI)

Query on NAP



Download:Ideal Coordinates CCD File
CA [auth G]
H [auth A]
K [auth B]
P [auth C]
T [auth D]
CA [auth G],
H [auth A],
K [auth B],
P [auth C],
T [auth D],
W [auth E],
Z [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
MMV
(Subject of Investigation/LOI)

Query on MMV



Download:Ideal Coordinates CCD File
AA [auth F]
DA [auth G]
I [auth A]
L [auth B]
Q [auth C]
AA [auth F],
DA [auth G],
I [auth A],
L [auth B],
Q [auth C],
U [auth D],
X [auth E]
3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid
C18 H24 N4 O4
VDGXZSSDCDPCRF-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth F]
EA [auth G]
M [auth B]
R [auth C]
V [auth D]
BA [auth F],
EA [auth G],
M [auth B],
R [auth C],
V [auth D],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
N [auth B],
O [auth B],
S [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.63α = 90
b = 62.49β = 94.67
c = 124.55γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Database references, Structure summary