1BZF

NMR SOLUTION STRUCTURE AND DYNAMICS OF THE COMPLEX OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE WITH THE NEW LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE, 22 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 22 
  • Conformers Submitted: 22 
  • Selection Criteria: NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate.

Polshakov, V.I.Birdsall, B.Frenkiel, T.A.Gargaro, A.R.Feeney, J.

(1999) Protein Sci 8: 467-481

  • DOI: https://doi.org/10.1110/ps.8.3.467
  • Primary Citation of Related Structures:  
    1BZF

  • PubMed Abstract: 

    We have determined the three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase and the anticancer drug trimetrexate. Two thousand seventy distance, 345 dihedral angle, and 144 hydrogen bond restraints were obtained from analysis of multidimensional NMR spectra recorded for complexes containing 15N-labeled protein. Simulated annealing calculations produced a family of 22 structures fully consistent with the constraints. Several intermolecular protein-ligand NOEs were obtained by using a novel approach monitoring temperature effects of NOE signals resulting from dynamic processes in the bound ligand. At low temperature (5 degrees C) the trimethoxy ring of bound trimetrexate is flipping sufficiently slowly to give narrow signals in slow exchange, which give good NOE cross peaks. At higher temperature these broaden and their NOE cross peaks disappear thus allowing the signals in the lower-temperature spectrum to be identified as NOEs involving ligand protons. The binding site for trimetrexate is well defined and this was compared with the binding sites in related complexes formed with methotrexate and trimethoprim. No major conformational differences were detected between the different complexes. The 2,4-diaminopyrimidine-containing moieties in the three drugs bind essentially in the same binding pocket and the remaining parts of their molecules adapt their conformations such that they can make effective van der Waals interactions with essentially the same set of hydrophobic amino acids, the side-chain orientations and local conformations of which are not greatly changed in the different complexes (similar chi1 and chi2 values).


  • Organizational Affiliation

    Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIHYDROFOLATE REDUCTASE162Lacticaseibacillus caseiMutation(s): 0 
EC: 1.5.1.3
UniProt
Find proteins for P00381 (Lacticaseibacillus casei)
Explore P00381 
Go to UniProtKB:  P00381
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00381
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TMQ
Query on TMQ

Download Ideal Coordinates CCD File 
B [auth A]TRIMETREXATE
C19 H24 N5 O3
NOYPYLRCIDNJJB-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
TMQ PDBBind:  1BZF Kd: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 22 
  • Conformers Submitted: 22 
  • Selection Criteria: NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-18
    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: Database references, Derived calculations, Other
  • Version 1.4: 2024-05-22
    Changes: Data collection