Rapid advancements in the experimental capabilities with ultracold alkaline-earth-like atoms (AEAs) bring to a surprisingly near term the prospect of performing quantum simulations of spin models and lattice field theories exhibiting SU(N) symmetry. Motivated in particular by recent experiments preparing high density samples of strongly interacting 87 Sr atoms in a three-dimensional optical lattice, we develop a low-energy effective theory of fermionic AEAs which exhibits emergent multibody SU(N)-symmetric interactions, where N is the number of atomic nuclear spin levels. Our theory is limited to the experimental regime of (i) a deep lattice, with (ii) at most one atom occupying each nuclear spin state on any lattice site. The latter restriction is a consequence of initial ground-state preparation. We fully characterize the low-lying excitations in our effective theory, and compare predictions of many-body interaction energies with direct measurements of many-body excitation spectra in an optical lattice clock. Our work makes the first step in enabling a controlled, bottom-up experimental investigation of multi-body SU(N) physics. 1 0 and P 3 0 states, AEAs exhibit decoupled orbital and OPEN ACCESS RECEIVED