1HFP

COMPARISON OF TERNARY CRYSTAL COMPLEXES OF HUMAN DIHYDROFOLATE REDUCTASE WITH NADPH AND A CLASSICAL ANTITUMOR FUROPYRIMDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Comparison of ternary crystal complexes of F31 variants of human dihydrofolate reductase with NADPH and a classical antitumor furopyrimidine.

Cody, V.Galitsky, N.Luft, J.R.Pangborn, W.Blakley, R.L.Gangjee, A.

(1998) Anti-Cancer Drug Des. 13: 307-315

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The novel furopyrimidine, N-[4-[(2,4-diaminofuro[2,3-d]pyrimidin-5-yl)-methyl]-methylamino] -benzoyl]-L-glutamate (MTXO), a classical antifolate with weak antitumor activity compared with methotrexate (MTX), has been studied as inhibitorcofactor tern ...

    The novel furopyrimidine, N-[4-[(2,4-diaminofuro[2,3-d]pyrimidin-5-yl)-methyl]-methylamino] -benzoyl]-L-glutamate (MTXO), a classical antifolate with weak antitumor activity compared with methotrexate (MTX), has been studied as inhibitorcofactor ternary crystal complexes with recombinant Phe-31 to Ser (F31S) and Phe-31 to Gly (F31G) variant human dihydrofolate reductase (hDHFR). Kinetic data show that the binding affinity of MTXO is significantly weaker for the variant hDHFR enzyme than for the wild type enzyme. Structural data for the Phe-31 variants, along with wild type hDHFR, provide the first direct comparison of the binding interactions of a single antifolate in a family of variant hDHFR. These ternary hDHFR complexes crystallize in the rhombohedral space group R3, isomorphous to that reported for wild type hDHFR MTXO-NADPH ternary complex. MTXO binds with its 2,4-diaminofuropyrimidine ring interacting with Glu-30 in hDHFR. The greatest change on modification of the side chain at position 31 is loss of hydrophobic contacts to the inhibitor, which results in the significant decrease in binding affinity of MTXO for the Phe-31 variants. The presence of the 6-5 furopyrimidine ring instead of the 6-6 pteridine ring causes a different bridge conformation compared with MTX, and in the case of the wild type MTXO complex also results in weaker hydrophobic contacts to Phe-31 than observed for MTXT. For the design of antitumor agents related to MTXO, increasing the bridge of MTXO from two to three or four atoms should provide increased DHFR inhibitory potency and antitumor activity.


    Related Citations: 
    • Comparison of Ternary Complexes of Pneumocystis Carinii and Wild-Type Human Dihydrofolate Reductase with a Novel Classical Antitumor Furo[2,3-D]Pyrimidine Antifolate
      Cody, V.,Galitsky, N.,Luft, J.R.,Pangborn, W.,Gangjee, A.,Devraj, R.,Queener, S.F.,Blakley, R.L.
      (1997) Acta Crystallogr.,Sect.D 53: 638
    • Methotrexate-Resistant Variants of Human Dihydrofolate Reductase with Substitutions of Leucine 22. Kinetics, Crystallography, and Potential as Selectable Markers
      Lewis, W.S.,Cody, V.,Galitsky, N.,Luft, J.R.,Pangborn, W.,Chunduru, S.K.,Spencer, H.T.,Appleman, J.R.,Blakley, R.L.
      (1995) J.Biol.Chem. 270: 5057
    • Methotrexate-Resistant Variants of Human Dihydrofolate Reductase. Effects of Phe31 Substitutions
      Chunduru, S.K.,Cody, V.,Luft, J.R.,Pangborn, W.,Appleman, J.R.,Blakley, R.L.
      (1994) J.Biol.Chem. 269: 9547
    • Crystal Structure Determination at 2.3 A of Recombinant Human Dihydrofolate Reductase Ternary Complex with Nadph and Methotrexate-Gamma-Tetrazole
      Cody, V.,Luft, J.R.,Ciszak, E.,Kalman, T.I.,Freisheim, J.H.
      (1992) Anti-Cancer Drug Des. 7: 483


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, Inc., NY 14203, USA. cody@hwi.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
186Homo sapiensMutation(s): 1 
Gene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Go to Gene View: DHFR
Go to UniProtKB:  P00374
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOT
Query on MOT

Download SDF File 
Download CCD File 
A
N-[4-[(2,4-DIAMINOFURO[2,3D]PYRIMIDIN-5-YL)METHYL]METHYLAMINO]-BENZOYL]-L-GLUTAMATE
C20 H22 N6 O6
WXINNGCGSCFUCR-ZDUSSCGKSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
COEIC50: 220 - 19800 nM (99) BINDINGDB
MOTKi: 1036 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.181 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 87.120α = 90.00
b = 87.120β = 90.00
c = 77.014γ = 120.00
Software Package:
Software NamePurpose
PROFFTrefinement
R-AXISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-12-11
    Type: Non-polymer description