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The Urban Disguise 30 won't fit the D3. The Urban Disguise 35 V2 has a small footprint, though it may be taller than what you're looking for.
I'm trying to think of what else that's in our product line that's sized for the gear you've listed, is small and isn't a holster and I'm can't think of anything off bat.
Just let me know if you have any other Think Tank Photo questions, though the folks around here do a great job of answering them before I do!