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 (
    62636, 62635, 62634, 62633, 62632, 62631, 
    62630, 62629, 62628, 62627, 62626, 
    62625, 62611, 62609, 62607, 62569, 
    62456, 61887, 60269, 62370, 62342, 
    62098, 62097, 61770, 61769, 61704, 
    60784, 60268, 62217, 61403, 61442, 
    62055, 61886, 61768, 60787, 60267, 
    62105, 61512, 62019, 61960
  ) 
  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 0.00065

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