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 (
    31436, 31435, 31434, 31433, 31432, 31431, 
    31430, 31429, 31428, 31427, 31426, 
    31425, 31424, 31423, 14017, 13990, 
    13989, 13968, 13987, 13986, 13985, 
    13983, 13982, 13981, 13980, 13979, 
    13978, 13977, 13976, 13975, 13974, 
    13973, 13972, 13971, 13970, 13969, 
    16527, 13892, 13891, 13882
  ) 
  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 0.00057

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