1NJS

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

Summary for 1NJS

• Entry DOI: 10.2210/pdb1njs/pdb
• Related: 1MEJ 1MEN 1MEO
• Descriptor: Phosphoribosylglycinamide formyltransferase, PHOSPHATE ION, 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, ... (4 entities in total)
• Functional Keywords: protein-cofactor analogue complex, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 46741.79

Authors

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. (deposition date: 2003-01-02, release date: 2003-06-10, Last modification date: 2023-08-16)

Primary citation

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.
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
Biochemistry, 42:6043-6056, 2003

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-5,6,7,8-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.

PubMed: 12755606
DOI: 10.1021/bi034219c

Experimental method

X-RAY DIFFRACTION (1.98 Å)