Grasping point detection has traditionally been a core robotic and computer vision problem. In recent years, deep learning based methods have been widely used to predict grasping points, and have shown strong generalization capabilities under uncertainty. Particularly, approaches that aim at predicting object affordances without relying on the object identity, have obtained promising results in random bin-picking applications. However, most of them rely on RGB/RGB-D images, and it is not clear up to what extent 3D spatial information is used. Graph Convolutional Networks (GCNs) have been successfully used for object classification and scene segmentation in point clouds, and also to predict grasping points in simple laboratory experimentation. In the present proposal, we adapted the Deep Graph Convolutional Network model with the intuition that learning from n-dimensional point clouds would lead to a performance boost to predict object affordances. To the best of our knowledge, this is the first time that GCNs are applied to predict affordances for suction and gripper end effectors in an industrial bin-picking environment. Additionally, we designed a bin-picking oriented data preprocessing pipeline which contributes to ease the learning process and to create a flexible solution for any bin-picking application. To train our models, we created a highly accurate RGB-D/3D dataset which is openly available on demand. Finally, we benchmarked our method against a 2D Fully Convolutional Network based method, improving the top-1 precision score by 1.8% and 1.7% for suction and gripper respectively.