We consider the problem of identification of linear dynamical systems from a single trajectory. Recent results have predominantly focused on the setup where no structural assumption is made on the system matrix $A^* \in \mathbb{R}^{n \times n}$, and have consequently analyzed the ordinary least squares (OLS) estimator in detail. We assume prior structural information on $A^*$ is available, which can be captured in the form of a convex set $\mathcal{K}$ containing $A^*$. For the solution of the ensuing constrained least squares estimator, we derive non-asymptotic error bounds in the Frobenius norm which depend on the local size of the tangent cone of $\mathcal{K}$ at $A^*$. To illustrate the usefulness of this result, we instantiate it for the settings where, (i) $\mathcal{K}$ is a $d$ dimensional subspace of $\mathbb{R}^{n \times n}$, or (ii) $A^*$ is $k$-sparse and $\mathcal{K}$ is a suitably scaled $\ell_1$ ball. In the regimes where $d, k \ll n^2$, our bounds improve upon those obtained from the OLS estimator.