There are several sites that will allow you to convert 2D drawings to 3D models (https://www.google.com/search?client=safari&rls=en&ei=Zip1XLHyFaK61fAPnLG_wAs&q=convert+2d+chemical+structure+to+3d&oq=convert+2d+chemical+structure+to+3d&gs_l=psy-ab.12..0i71l8.0.0..4154...0.0..0.0.0.......0......gws-wiz.MH3wHo_7C7g). For essentially planar ring systems this is easy, for puckered rings and more flexible structures it may be more tricky, as several conformers may be populated to varying degree. You can also use WebCSD for crystal structures of organic molecules (The cambridge crystallographic data center, https://www.ccdc.cam.ac.uk/structures/WebCSD/StructureSearch).

Depending on what you want to do with your structure, .pdb might not be the best format to use, as it does not generally retain such informations as bond order and charges -better keep small molecules in .sdf, .mol or mol2 format. For nucleic acids and proteins, the pdf format relies on molecular dictionaries in the interpreting programs to fill in missing chemical data for nucleotide and amino acid residues.