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 (
    89607, 89606, 89605, 89604, 89603, 89602, 
    89601, 89600, 90393, 90163, 90070, 
    90069, 90068, 89588, 89587, 89535, 
    89534, 90287, 89533, 90328, 90327, 
    89543, 89530, 89529, 89528, 89517, 
    89487, 89486, 90303, 90302, 90301, 
    90300, 90299, 90298, 90297, 90296, 
    90295, 90294, 90293, 90292
  ) 
  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 0.00055

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