The 3D structures of a large variety of biologically important small molecules as well as their PDB format files can be found at the Klothos web link.
Download the windows version of RASMOL to look at PDB (protein databank) and MOL files
| a Amino Acids (all L) | Cofactors and coenzymes |
| Aspartic acid ASP D | S-adenosylmethionine (SAM) |
| Asparagine ASN N | NAD+, NADH, NADP+, NADPH |
| Glutamic acid GLU E | ATP, ADP, AMP |
| Glutamine GLN Q | Coenzyme A (CoA) |
| Lysine LYS K | acetylCoA |
| Arginine ARG R | biotin |
| Tryptophan TRP W | thiamine |
| Tyrosine TYR Y | pyrodoxal phosphate (PLP) |
| Phenylalanine PHE F | FAD, FADH2, FMN, FMNH2, riboflavin |
| Proline PRO P | lipoic acid |
| Histidine HIS H | tetrahydofolic acid (THF) |
| Alanine ALA A | ubiquinone |
| Leucine LEU L | creatine phosphate |
| Isoleucine ILE I | Fe-protoporphyrin IX (heme) |
| Valine VAL V | cyanocobalamin (vitamin B12) |
| Threonine THR T | chlorophyll a |
| Serine SER S | Nucleic acids |
| Methionine MET M | uracil U |
| Cysteine CYS C | adenine A |
| Glycine GLY G | cytosine C |
| Cystine | guanine G |
| Carbohydrates, Carboxylic acids | thymine T |
| D-ribose | nucleotides and nucleoside of the above |
| D-glucose | Important linkages |
| D-fructose | peptide, amide |
| D-fructose-6-phosphate | thioester |
| D-fructose-1,6-bisphosphate | phosphodiester |
| sucrose | glycosidic |
| D-glyceraldehyde-3-phosphate | |
| dihydroxyacetone phosphate | biochemical pathways |
| phosphoenol pyruvate | glycolysis |
| pyruvate | Krebs cycle, tricarboxylic acid cycle |
| lactate | oxidative phosphorylation |
| citrate | calvin cycle |
| cis-aconitate | photosynthesis |
| 2R-3S isocitrate | |
| acetic acid | |
| a-ketoglutarate | |
| succinate | |
| malate | |
| fumarate | |
| ascorbate | |
| oxaloacetate |