4IXF

pcDHFR-269 F69N variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, and Molecular Modeling of Novel Pyrido[2,3-d]pyrimidine Analogues As Antifolates; Application of Buchwald-Hartwig Aminations of Heterocycles.

Gangjee, A.Namjoshi, O.A.Raghavan, S.Queener, S.F.Kisliuk, R.L.Cody, V.

(2013) J.Med.Chem. 56: 4422-4441

  • DOI: 10.1021/jm400086g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Opportunistic infections caused by Pneumocystis jirovecii (P. jirovecii, pj), Toxoplasma gondii (T. gondii, tg), and Mycobacterium avium (M. avium, ma) are the principal causes of morbidity and mortality in patients with acquired immunodeficiency syn ...

    Opportunistic infections caused by Pneumocystis jirovecii (P. jirovecii, pj), Toxoplasma gondii (T. gondii, tg), and Mycobacterium avium (M. avium, ma) are the principal causes of morbidity and mortality in patients with acquired immunodeficiency syndrome (AIDS). The absence of any animal models for human Pneumocystis jirovecii pneumonia and the lack of crystal structures of pjDHFR and tgDHFR make the design of inhibitors challenging. A novel series of pyrido[2,3-d]pyrimidines as selective and potent DHFR inhibitors against these opportunistic infections are presented. Buchwald-Hartwig coupling reaction of substituted anilines with pivaloyl protected 2,4-diamino-6-bromo-pyrido[2,3-d]pyrimidine was successfully explored to synthesize these analogues. Compound 26 was the most selective inhibitor with excellent potency against pjDHFR. Molecular modeling studies with a pjDHFR homology model explained the potency and selectivity of 26. Structural data are also reported for 26 with pcDHFR and 16 and 22 with variants of pcDHFR.


    Organizational Affiliation

    Division of Medicinal Chemistry, Graduate School Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA. gangjee@duq.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
X
206Pneumocystis cariniiMutation(s): 1 
EC: 1.5.1.3
Find proteins for P16184 (Pneumocystis carinii)
Go to UniProtKB:  P16184
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IXF
Query on IXF

Download SDF File 
Download CCD File 
X
N~6~-methyl-N~6~-[4-(propan-2-yl)phenyl]pyrido[2,3-d]pyrimidine-2,4,6-triamine
C17 H20 N6
CRSDIJKYSOUKQH-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
X
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.365α = 90.00
b = 42.749β = 95.46
c = 60.918γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-01-25 
  • Released Date: 2013-05-29 
  • Deposition Author(s): Cody, V.

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description