SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    2591, 1042, 1534, 41231, 5833, 31641, 
    400, 5835, 6089, 27363, 6562, 1781, 
    3885, 33716, 5836, 25733, 35734, 6068, 
    33717, 5507, 36781, 2563, 37305, 2566, 
    3384, 38146, 41435, 5505, 31643, 2415, 
    144, 2564
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00521

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (2591,1042,1534,41231,5833,31641,400,5835,6089,27363,6562,1781,3885,33716,5836,25733,35734,6068,33717,5507,36781,2563,37305,2566,3384,38146,41435,5505,31643,2415,144,2564)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}