Abstract A dihydropyrimidine (DHPM) derivative was synthesized, characterized by X-ray diffraction and searched in silico for its inhibitory activities against AccD5 enzyme, the CT domain of a Mycobacterium tuberculosis ACCase. Its molecular structure was compared to another DHPM derivative (DHPM II). The results have shown that the (±)2,6-methano-4-thioxo-3,4,5,6-tetrahydro-2H-[1,3,5] benzoxadiazocines (DHPM I) and (±)2,6-methano-4-oxo-3,4,5,6-tetrahydro-2H-[1,3,5] benzoxadiazocines (DHPM II) belong to the monoclinic and triclinic systems, respectively, and their crystal structures are stabilized by N–H⋯O, O–H⋯O and N–H⋯S interactions. The DHPM derivatives established hydrogen bond interactions with the oxyanion-stabilizing residues (Gly-434/Ala-435) beyond the Thr-217, Phe-394 and Ile-216 in the biotin pocket. The predicted MoB of the DHPM derivatives (21R, 24S, 22R) configuration showed that its phenyl moiety was positioned on the interface between the biotin and propionyl-CoA pockets, suggesting a possible blockade of both subsites. Additionally, the hydrogen bonds involving the O-bridged phenyl ring of the DHPM derivatives (21S, 24R, 22S) configuration with Gly434 in the oxyanion-stabilizing region placed its phenyl moiety in the bottom of the biotin pocket establishing hydrophobic interactions with Leu164, Tyr167, Val459 and Ala155. These results indicate the DHPM derivatives as potential AccD5 inhibitors and promising starting points for future optimizations. Although the overlap of DHPM I and DHPM II did not present significant differences, the exchange of a sulfur atom for an oxygen atom increased the predicted biological potential.