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 (
    65260, 65340, 65210, 64553, 65258, 65257, 
    65256, 65255, 65254, 65253, 65252, 
    65251, 65250, 65249, 65248, 65247, 
    65246, 65245, 65244, 65243, 65242, 
    65241, 65240, 65239, 65238, 65237, 
    65236, 65235, 65234, 65233, 65232, 
    65231, 65230, 65229, 65163, 65162, 
    65161, 65160, 65159, 65114
  ) 
  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 0.00069

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