1NJS

human GAR Tfase in complex with hydrolyzed form of 10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rational Design, Synthesis, Evaluation, and Crystal Structure of a Potent Inhibitor of Human GAR Tfase: 10-(Trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic Acid

Zhang, Y.Desharnais, J.Marsilje, T.H.Li, C.Hedrick, M.P.Gooljarsingh, L.T.Tavassoli, A.Benkovic, S.J.Olson, A.J.Boger, D.L.Wilson, I.A.

(2003) Biochemistry 42: 6043-6056

  • DOI: 10.1021/bi034219c
  • Primary Citation of Related Structures:  
    1NJS

  • PubMed Abstract: 
  • Glycinamide ribonucleotide transformylase (GAR Tfase) has been the target of anti-neoplastic intervention for almost two decades. Here, we use a structure-based approach to design a novel folate analogue, 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6, ...

    Glycinamide ribonucleotide transformylase (GAR Tfase) has been the target of anti-neoplastic intervention for almost two decades. Here, we use a structure-based approach to design a novel folate analogue, 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid (10-CF(3)CO-DDACTHF, 1), which specifically inhibits recombinant human GAR Tfase (K(i) = 15 nM), but is inactive (K(i) > 100 microM) against other folate-dependent enzymes that have been examined. Moreover, compound 1 is a potent inhibitor of tumor cell proliferation (IC(50) = 16 nM, CCRF-CEM), which represents a 10-fold improvement over Lometrexol, a GAR Tfase inhibitor that has been in clinical trials. Thus, this folate analogue 1 is among the most potent and selective inhibitors known toward GAR Tfase. Contributing to its efficacious activity, compound 1 is effectively transported into the cell by the reduced folate carrier and intracellularly sequestered by polyglutamation. The crystal structure of human GAR Tfase with folate analogue 1 at 1.98 A resolution represents the first structure of any GAR Tfase to be determined with a cofactor or cofactor analogue without the presence of substrate. The folate-binding loop of residues 141-146, which is highly flexible in both Escherichia coli and unliganded human GAR Tfase structures, becomes highly ordered upon binding 1 in the folate-binding site. Computational docking of the natural cofactor into this and other apo or complexed structures provides a rational basis for modeling how the natural cofactor 10-formyltetrahydrofolic acid interacts with GAR Tfase, and suggests that this folate analogue-bound conformation represents the best template to date for inhibitor design.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoribosylglycinamide formyltransferaseAB209Homo sapiensMutation(s): 0 
Gene Names: GARTPGFTPRGS
EC: 2.1.2.2 (PDB Primary Data), 6.3.4.13 (UniProt), 6.3.3.1 (UniProt)
Find proteins for P22102 (Homo sapiens)
Explore P22102 
Go to UniProtKB:  P22102
NIH Common Fund Data Resources
PHAROS  P22102
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KEU
Query on KEU

Download CCD File 
A, B
N-{4-[(1R)-4-[(2R,4R,5S)-2,4-DIAMINO-6-OXOHEXAHYDROPYRIMIDIN-5-YL]-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXYETHYL)BUTYL]BENZOYL}-D-GLUTAMIC ACID
C22 H30 F3 N5 O8
KOLDLUFBEMUZIM-YNPGLMGXSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KEUKi:  15   nM  Binding MOAD
KEUKi :  15   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.235α = 90
b = 126.235β = 90
c = 94.419γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance