Selectins interact with cell-surface glycans to promote the initial tethering and rolling of leukocytes, and these interactions are targets for designs of inhibitors to neutralize diseases related to excessive inflammatory responses in many cardiovascular and immune dysfunctions, as well as tumor markers in different cancers. The isomeric endogenous tetrasaccharides, sialyl Lewis X (sLex) and sialyl Lewis A (sLea), are minimal sugar structures required for selectin binding. Understanding their subtle structural variances and significant advanced binding strengths of sLea over sLex could benefit the rational designs for selectin inhibitors. Modeling based on the E-selectin-sLex crystal structure in the present study demonstrated that the N-acetyl group of GlcNAc in sLex could form steric hindrances in the E-selectin-sLex complex, but the hydroxy methylene group of GlcNAc in sLea at the same position allows for stronger binding interactions. The subsequent designed inhibitor with a synthetic accessible linker molecule that has no exo-cyclic moieties replacing GlcNAc displayed comparable dynamic and energetic binding features to sLea. The present study deciphered the clues from endogenous isomeric sLea and sLex and provided insights into designing selectin inhibitors with simplified synthesis.