1DIS

DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEX WITH BRODIMOPRIM-4,6-DICARBOXYLATE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase.

Morgan, W.D.Birdsall, B.Polshakov, V.I.Sali, D.Kompis, I.Feeney, J.

(1995) Biochemistry 34: 11690-11702

  • DOI: 10.1021/bi00037a006
  • Primary Citation of Related Structures:  
    1DIS, 1DIU

  • PubMed Abstract: 
  • Two-dimensional (2D) double-quantum-filtered correlation spectroscopy (DQF-COSY), total correlation spectroscopy (TOCSY), nuclear Overhauser effect spectroscopy (NOESY), and rotating-frame NOESY (ROESY) spectra were used to assign essentially all the protons in a 1:1 complex of Lactobacillus casei dihydrofolate reductase formed with an analogue of the antibacterial drug brodimoprim [2,4-diamino-5-(3',5'-dimethoxy-4'-bromobenzyl)pyrimidine] ...

    Two-dimensional (2D) double-quantum-filtered correlation spectroscopy (DQF-COSY), total correlation spectroscopy (TOCSY), nuclear Overhauser effect spectroscopy (NOESY), and rotating-frame NOESY (ROESY) spectra were used to assign essentially all the protons in a 1:1 complex of Lactobacillus casei dihydrofolate reductase formed with an analogue of the antibacterial drug brodimoprim [2,4-diamino-5-(3',5'-dimethoxy-4'-bromobenzyl)pyrimidine]. The analogue has a 4,6-dicarboxylic acid side chain substituted on the 3'-O position designed to interact with the Arg 57 and His 28 residues in L. casei dihydrofolate reductase; it binds a factor of 10(3) more tightly to the enzyme than does the parent compound. Thirty-eight intermolecular and 11 intramolecular NOEs were measured involving the bound brodimoprim-4,6-dicarboxylic acid analogue. These provided the distance constraints used in conjunction with an energy minimization and simulated annealing protocol (using Discover from Biosym Ltd.) to dock the brodimoprim analogue into dihydrofolate reductase. In calculations where side chains and backbone fragments for binding-site residues were allowed flexibility, 90% of the 40 calculated structures had reasonable covalent geometry and none of them had NOE distance violations of greater than 0.36 A. The conformations of the aromatic rings in the bound ligand were well-defined in all the structures, with torsion angles tau 1 = -153 degrees +/- 4 degrees (C4-C5-C7-C1') and tau 2 = 53 degrees +/- 4 degrees (C5-C7-C1'-C2'): the aromatic rings of the ligand occupied essentially the same space in all the calculated structures (root mean square deviation value 1.83 A). Inclusion of the electrostatic interactions into the energy minimizations indicated that structures in which the 4,6-dicarboxylate group of the ligand interacts with the side chains of Arg 57 and His 28 are of low energy. Significant differences in side-chain and backbone conformations were detected between binding-site residues in the enzyme complexes with the brodimorpim analogue and methotrexate.


    Related Citations: 
    • Solution Structure of Bound Trimethoprim in its Complex with Lactobacillus Casei Dihydrofolate Reductase
      Martorell, G., Gradwell, M.J., Birdsall, B., Bauer, C.J., Frenkiel, T.A., Cheung, H.T.A., Polshakov, V.I., Kuyper, L., Feeney, J.
      (1994) Biochemistry 33: 12416
    • A 1H NMR Study of the Interactions and Conformations of Rationally Designed Brodimoprim Analogues in Complexes with Lactobacillus Casei Dihydrofolate Reductase
      Birdsall, B., Feeney, J., Pascual, C., Roberts, G.C.K., Kompis, I., Then, R.L., Mueller, K., Kroehn, A.
      (1984) J Med Chem 27: 1672
    • Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
      Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., Kraut, J.
      (1982) J Biol Chem 257: 13650

    Organizational Affiliation

    Laboratory of Molecular Structure, National Institute for Medical Research, Mill Hill, London, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASEA162Lacticaseibacillus caseiMutation(s): 0 
Gene Names: POTENTIALfolAdhfR
EC: 1.5.1.3
UniProt
Find proteins for P00381 (Lactobacillus casei)
Explore P00381 
Go to UniProtKB:  P00381
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00381
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BDM
Query on BDM

Download Ideal Coordinates CCD File 
B [auth A]BRODIMOPRIM-4,6-DICARBOXYLATE
C20 H24 Br N4 O6
SZAVCZNFKJSWRN-LBPRGKRZSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BDM PDBBind:  1DIS Ki: 1.00e-2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary