Unity from the Sybyl package was used for pharmacophore filtering. Pharmacophoric points were defined protein based code 2v8p) with default settings to include the desired directionalities for hydrogen bonding. The initial pharmacophore search was performed with flexible ligand molecules, allowing rotation and conformational changes to match the required features. At least two of the possible four features had to be fulfilled to pass this filter. For filtering the docking poses, the docked ligands were kept rigid and no translations and rotations were allowed. A database containing all compounds passing the pharmacophore filter step in a format suitable for docking and considering multiple protonation states and tautomers was prepared as described previously. The AaIspE crystal structure was the receptor for docking. Four different setups were prepared taking into account the possible tautomers of His25, and the presence or absence of the co-factor. Polar hydrogen atoms were added to the receptor and their positions minimised using the MAB force field as implemented in MOLOC. Partial charges for the co-factor were calculated using AMSOL. Spheres as matching points for docking were placed around the cytidine heterocycle of the bound substrate. The sphere set defining the buried region of the binding site was generated around the whole substrate and cofactor. Grids to store information about excluded volumes, electrostatic and van der Waals potential, and solvent occlusion were calculated as described earlier. Each docking pose which did not place any atoms in areas occupied by the receptor was scored for electrostatic and van der Waals complementarity and Lapatinib penalised according to its estimated partial desolvation energy. The docking setup was validated by successful predictions of the binding modes of CDP, CDP-ME, and cytosine. For each compound in the screening database, only the best-scoring representation was stored in the final docking hit list. Cytidine analogues such as gemcitabine are widely used to treat a variety of cancers. Gemcitabine remains standard therapy for pancreatic cancer in the adjuvant and palliative settings. However, the gemcitabine response rate is very low in pancreatic cancer, with only an 18% 1 year survival rate. This poor survival rate is primarily because of the lack of early detection and frequent metastasis of primary tumors into lymph nodes and surrounding organs, such as the liver and stomach. As a step toward individualized gemcitabine therapy in order to achieve better outcomes, we previously performed a genome wide association study using 197 individual lymphoblastoid cell lines and identified a protein, FKBP5, that showed a significant effect on gemcitabine response in tumor cells by negatively regulating Akt phosphorylation at serine 473. Phosphorylation of Akt activates the Akt pathway, which plays a critical role in tumorigenesis and chemoresistance. Therefore, low FKBP5 expression renders tumor cells resistant to many chemotherapeutic agents, including gemcitabine. In addition, FKBP5 expression is low or lost in many pancreatic cancer cell lines and pancreatic cancer patient samples, correlating with increased Akt Ser473 phosphorylation. These results suggested that FKBP5 might be a tumor suppressor and that levels of FKBP5 might determine patients’ response to TWS119 chemotherapy. If that is correct, patients with low levels of FKBP5 and Akt hyperactivation might benefit from the addition of inhibitors targeting the Akt pathway. In the current study, we tested that hypothesis by using an FKBP5 knockdown pancreatic cancer xenograft mouse model and the results of these experiments may form a foundation for future clinical translational studies.