The crystal structure of the FMN containing redox partner to P450cin, cindoxin (Cdx), has been solved to 1.3 Å resolution. The overall structure is similar to the FMN domain of human cytochrome P450 reductase. A Brownian dynamics/molecular dynamics docking method was used to produce a model of Cdx with its redox partner, P450cin. This Cdx-P450cin model highlights the potential importance of Cdx Tyr96 in bridging the FMN and heme cofactors as well P450cin Arg102 and Arg346. Each of the single site Ala mutants exhibit about 10% wild type activity thus demonstrating the importance of these residues for binding and/or electron transfer. In the well studied P450cam system, redox partner binding stabilizes the open low-spin conformation of P450cam and decreases the stability of the oxy-complex by 150 fold. In sharp contrast, Cdx does not shift P450cin to low-spin although the stability of oxy-P450cin is decreased 10-fold in the presence of Cdx. This indicates that Cdx may have a modest effect on the open/close equilibrium in P450cin compared to P450cam. It has been postulated that part of the effector role of Pdx on P450cam is to promote a significant structural change that makes available a proton relay network involving Asp251 required for O2 activation. The structure around the corresponding Asp in P450cin, Asp241, provides a possible structural reason why P450cin is less dependent on its redox partner for functionally important structural changes.