6VCJ

Crystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

The Structural Basis for Nonsteroidal Anti-Inflammatory Drug Inhibition of Human Dihydrofolate Reductase.

Duff Jr., M.R.Gabel, S.A.Pedersen, L.C.DeRose, E.F.Krahn, J.M.Howell, E.E.London, R.E.

(2020) J Med Chem 63: 8314-8324

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00546
  • Primary Citation of Related Structures:  
    6VCJ

  • PubMed Abstract: 

    Although nonsteroidal anti-inflammatory drugs (NSAIDs) target primarily cyclooxygenase enzymes, a subset of NSAIDs containing carboxylate groups also has been reported to competitively inhibit dihydrofolate reductase (DHFR). In this study, we have characterized NSAID interactions with human DHFR based on kinetic, NMR, and X-ray crystallographic methods. The NSAIDs target a region of the folate binding site that interacts with the p -aminobenzoyl-l-glutamate (pABG) moiety of folate and inhibit cooperatively with ligands that target the adjacent pteridine-recognition subsite. NSAIDs containing benzoate or salicylate groups were identified as having the highest potency. Among those tested, diflunisal, a salicylate derivative not previously identified to have anti-folate activity, was found to have a K i of 34 μM, well below peak plasma diflunisal levels reached at typical dosage levels. The potential of these drugs to interfere with the inflammatory process by multiple pathways introduces the possibility of further optimization to design dual-targeted analogs.


  • Organizational Affiliation

    Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase
A, B, C, D
188Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
PHAROS:  P00374
GTEx:  ENSG00000228716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00374
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 
G [auth A],
K [auth B],
O [auth C],
S [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
FOL
Query on FOL

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D]
FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
NPX (Subject of Investigation/LOI)
Query on NPX

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D]
(2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid
C14 H14 O3
CMWTZPSULFXXJA-SECBINFHSA-N
LG3 (Subject of Investigation/LOI)
Query on LG3

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
Q [auth D]
PYRIMIDINE-2,4-DIAMINE
C4 H6 N4
YAAWASYJIRZXSZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NPX Binding MOAD:  6VCJ Ki: 1.10e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.397α = 90
b = 124.457β = 96.346
c = 84.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES050111
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES102645

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description