Drug discovery is a complex, resource-intensive process requiring significant time and cost to bring new medicines to patients. Many generative models aim to accelerate drug discovery, but few produce synthetically accessible molecules. Conversely, synthesis-focused models do not leverage the 3D information crucial for effective drug design. We introduce SynthFormer, a novel machine learning model that generates fully synthesizable molecules, structured as synthetic trees, by introducing both 3D information and pharmacophores as input. SynthFormer features a 3D equivariant graph neural network to encode pharmacophores, followed by a Transformer-based synthesis-aware decoding mechanism for constructing synthetic trees as a sequence of tokens. It is a first-of-its-kind approach that could provide capabilities for designing active molecules based on pharmacophores, exploring the local synthesizable chemical space around hit molecules and optimizing their properties. We demonstrate its effectiveness through various challenging tasks, including designing active compounds for a range of proteins, performing hit expansion and optimizing molecular properties.