A "sinister side" for me would be a ruthless side. Charming or not, this character would cross dead bodies for something and feel no remorse. It could be building houses on polluted and unfit ground for profit; it could be killing someone and eating their liver; it could be blowing up up a building full of civilians for a Cause.

The sinister aspect for me, would be the whiff of that ruthlessness, that complete feeling of entitlement, that makes this character do those things and not even question the basic premise that only his wishes matters and that others are pawns to be used and abused according to his wishes. It's about, IMO, giving the reader glimpses into the dark void that lies beneath the charming exterior. I think it's about giving the reader a little vertigo by allowing brief glimpses into just how far he could go. That can be done very subtly; with gestures, in trivial choices, in conversation or by bursts of sudden repulsive actions.

Someone mentioned The Prisoner of Zenda - I haven't seen that, but I've read it and Rupert is very charming, handsome and funny, but he also kills friends and foes without feeling any sort of remorse, and that's made obvious pretty early on. Once that's established (through his actions) he's a Charming Villain™.