A YDR file is GTA V's drawable model format. It contains the actual 3D mesh, materials and skinning data for a single model - a building, a vehicle part, a prop, a piece of geometry. Glossary anchor.
If a YMAP says 'place this object here', the YDR is the object.
What YDRs hold
Vertex and index data. Material assignments. Skeleton data for animated objects. Texture references. LOD geometry for distance rendering. The whole package needed to draw a model.
Custom 3D content for GTA - new buildings, new MLO interiors - ends up in YDR form via export plugins from 3ds Max or Blender.