In the present paper we investigate noncommutativity of $D9$ and $D5$-brane world-volumes embedded in space-time of type IIB superstring theory. Boundary conditions, which preserve half of the initial supersymmetry, are treated as canonical constraints. Solving the constraints we obtain original coordinates in terms of the effective coordinates and momenta. Presence of momenta induces noncommutativity of string endpoints. We show that noncommutativity relations are connected by N=1 supersymmetry transformations and noncommutativity parameters are components of N=1 supermultiplet.