10QV

Crystal Structure of NQO1 Complexed with S-Warfarin

Summary for 10QV

• Entry DOI: 10.2210/pdb10qv/pdb
• Descriptor: NAD(P)H dehydrogenase [quinone] 1, FLAVIN-ADENINE DINUCLEOTIDE, S-WARFARIN, ... (4 entities in total)
• Functional Keywords: cytoplasmic flavoprotein, antioxidant, flavoprotein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 4
• Total formula weight: 135766.40

Authors

Corrigan, M.C.,Vargas, A.L.,Moran, G.R.,Liu, D. (deposition date: 2026-02-02, release date: 2026-07-08, Last modification date: 2026-07-15)

Primary citation

Alt, T.B.,Corrigan, M.C.,Krawczykowski, K.J.,Smith, C.O.,Vargas, A.L.,Liu, D.,Moran, G.R.
Structural and kinetic analysis of human NQO1: Evidence for therapeutic inhibition by racemic warfarin.
Arch.Biochem.Biophys., 783:110911-110911, 2026

PubMed Abstract: The NAD(P)H:quinone oxidoreductase (NQO1) has also been described as DT-diaphorase and vitamin K reductase. This enzyme serves to reduce quinones including menadiones (vitamin K derivatives). This activity is thought to suppress the reactivity of the soluble quinone pool by accumulation of less reactive hydroquinols. Though it has been alluded to, the role of NQO1 in vitamin K recycling during thrombosis has not been definitively accounted for. Using transient-state kinetics methods, equilibrium titration and X-ray structural methods, we have examined both the observable catalytic steps of human NQO1 reacting with ubiquinone and the interaction of the enzyme with the anticoagulant, warfarin. These data show that the rate of turnover was governed primarily by the rate of release of ubiquinol. The reductive half-reaction data indicated a limiting rate of reduction of the active site flavin of ∼1300 s, while reoxidation of the flavin by the reduction of ubiquinone was too rapid to be observed by rapid mixing methods and so must occur at >2000 s. The rate of ubiquinol release however was measured by competition with the process of reduction by NADH and was found to be ∼370 s; a value consistent with the measured turnover number of ∼350 s. The reduction potential of the active site FAD cofactor was measured as quite positive at -138 mV and the stereochemistry of the hydride transfer of the reductive half reaction was confirmed from kinetic isotope effects using NADH isomers as ProR. It was also shown that both the S and R isomers of warfarin bind tightly to NQO1 suppressing activity by competing with the binding of native substrates. The structure of the NQO1•S-warfarin complex was solved to 1.8 Å resolution and revealed a binding mode similar to that previously observed for dicoumarol.

PubMed: 42362135
DOI: 10.1016/j.abb.2026.110911

Experimental method

X-RAY DIFFRACTION (1.9 Å)