SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    64531, 63919, 63727, 64535, 64525, 64524, 
    64509, 64424, 64100, 64099, 63197, 
    64508, 64507, 64506, 64505, 64429, 
    64428, 64427, 64426, 64425, 64393, 
    64208, 63573, 63572, 61775, 61755, 
    64145, 64122, 64121, 64120, 61891, 
    64080, 64079, 63775, 63898, 63897, 
    63871, 63718, 63301, 63300
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00061

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where