Quinic acid (1) and its derivative shikimic acid (2) are known to be key intermediates during the biochemical synthesis of essential aromatic amino acids in plants and bacteria and have led to extensive research activities. Potent anti-influenza A+B effect has been observed for derivatives of shikimic acid and has resulted in commercialization of the anti-flu medication TamifluTM (Roche). In this paper, we present Nuclear Overhauser Effect (NOE) build-up NMR data in combination with molecular dynamics simulation for two diastereomers of compound 3. Very good agreement between the experimental and theoretical data was observed. Our data allowed an estimation of the time-averaged H-H-distances and a general solution conformation of the molecules. The chemical removal of the benzylidene and iso-propylidene protection groups towards global deprotection was also investigated by Thin-Layer Chromatography (TLC) and Matrix-Assisted Laser Desorption/Ionization (MALDI) Time-Of-Flight (TOF) mass spectrometry.