Crystal structure of a methotrexate-resistant mutant of human dihydrofolate reductase

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.179 

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Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance.

Volpato, J.P.Yachnin, B.J.Blanchet, J.Guerrero, V.Poulin, L.Fossati, E.Berghuis, A.M.Pelletier, J.N.

(2009) J Biol Chem 284: 20079-20089

  • DOI: https://doi.org/10.1074/jbc.M109.018010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methotrexate is a slow, tight-binding, competitive inhibitor of human dihydrofolate reductase (hDHFR), an enzyme that provides key metabolites for nucleotide biosynthesis. In an effort to better characterize ligand binding in drug resistance, we have previously engineered hDHFR variant F31R/Q35E. This variant displays a >650-fold decrease in methotrexate affinity, while maintaining catalytic activity comparable to the native enzyme. To elucidate the molecular basis of decreased methotrexate affinity in the doubly substituted variant, we determined kinetic and inhibitory parameters for the simple variants F31R and Q35E. This demonstrated that the important decrease of methotrexate affinity in variant F31R/Q35E is a result of synergistic effects of the combined substitutions. To better understand the structural cause of this synergy, we obtained the crystal structure of hDHFR variant F31R/Q35E complexed with methotrexate at 1.7-A resolution. The mutated residue Arg-31 was observed in multiple conformers. In addition, seven native active-site residues were observed in more than one conformation, which is not characteristic of the wild-type enzyme. This suggests that increased residue disorder underlies the observed methotrexate resistance. We observe a considerable loss of van der Waals and polar contacts with the p-aminobenzoic acid and glutamate moieties. The multiple conformers of Arg-31 further suggest that the amino acid substitutions may decrease the isomerization step required for tight binding of methotrexate. Molecular docking with folate corroborates this hypothesis.

  • Organizational Affiliation

    Département de Biochimie, Université de Montréal, Montréal, Québec, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase186Homo sapiensMutation(s): 2 
Gene Names: DHFRDHFRP1
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MTX

Download Ideal Coordinates CCD File 
C20 H22 N8 O5
Query on CD

Download Ideal Coordinates CCD File 
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
MTX Binding MOAD:  3EIG Ki: 21 (nM) from 1 assay(s)
BindingDB:  3EIG Ki: min: 3.40e-4, max: 3.4 (nM) from 14 assay(s)
Kd: 0.19 (nM) from 1 assay(s)
IC50: min: 0.6, max: 1500 (nM) from 63 assay(s)
EC50: min: 12.5, max: 13.3 (nM) from 2 assay(s)
PDBBind:  3EIG Ki: 21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.348α = 90
b = 47.868β = 90
c = 90.715γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description