Endoscopy is the gold standard procedure for early detection and treatment of numerous diseases. Obtaining 3D reconstructions from real endoscopic videos would facilitate the development of assistive tools for practitioners, but it is a challenging problem for current Structure From Motion (SfM) methods. Feature extraction and matching are key steps in SfM approaches, and these are particularly difficult in the endoscopy domain due to deformations, poor texture, and numerous artifacts in the images. This work presents a novel learned model for feature extraction in endoscopy, called SuperPoint-E, which improves upon existing work using recordings from real medical practice. SuperPoint-E is based on the SuperPoint architecture but it is trained with a novel supervision strategy. The supervisory signal used in our work comes from features extracted with existing detectors (SIFT and SuperPoint) that can be successfully tracked and triangulated in short endoscopy clips (building a 3D model using COLMAP). In our experiments, SuperPoint-E obtains more and better features than any of the baseline detectors used as supervision. We validate the effectiveness of our model for 3D reconstruction in real endoscopy data. Code and model: https://github.com/LeonBP/SuperPointTrackingAdaptation.