The binding of the substrate NADPH as well as a number of fragments and derivatives of NADPH to glutathione reductase from human erythrocytes has been investigated by using X-ray crystallography. Crystals of the enzyme were soaked with the compounds of interest, and then the diffraction intensities were collected out to a resolution of 3 A. By use of phase information from the refined structure of the native enzyme in its oxidized state, electron density maps could be calculated. Difference Fourier electron density maps with coefficients Fsoak - Fnative showed that the ligands tested bound either at the functional NADPH binding site or not at all. Electron density maps with coefficients 2Fsoak - Fnative were used to estimate occupancies for various parts of the bound ligands. This revealed that all ligands except NADPH and NADH, which were fully bound, showed differential binding between the adenine end and the nicotinamide end of the molecule: The adenine end always bound with a higher occupancy than the nicotinamide end. Models were built for the protein-ligand complexes and subjected to restrained refinement at 3-A resolution. The mode of binding of NADPH, including the conformational changes of the protein, is described. NADH binding is clearly shown to involve a trapped inorganic phosphate at the position normally occupied by the 2'-phosphate of NADPH. A comparison of the binding of NADPH with the binding of the fragments and analogues provides a structural explanation for their relative binding affinities. In this respect, proper charge and hydrogen-bonding characteristics of buried parts of the ligand seem to be particularly important.