Zakir was born in 1784 in a noble family of bey in Panahabad, then the capital of the Karabakh khanate.
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His father Azad Khan Javanshir was the great grandson of the founder of Karabakh Khanate Panah Ali Khan.
Agha Muhammad was assassinated in 1797 in the city of Shusha, the capital of Karabakh khanate, less than 3 years in power.
His grand grandfather Kazim-agha was the brother of Panah Ali khan – the founder of and the Karabakh khanate and its capital Shusha.
Zakir belonged to the clan of Javanshir, which was the ruling clan in the Karabakh khanate.