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 (5, 3, 2) 
  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 0.00511

JSON explain

{
  "query_block": {
    "select_id": 1,
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "ref",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "lower_limit",
        "used_key_parts": [
          "lower_limit"
        ],
        "key_length": "3",
        "ref": [
          "const"
        ],
        "rows": 6,
        "filtered": 100,
        "attached_condition": "((`_testcscart`.`cscart_product_prices`.`lower_limit` <=> 1) and ((`_testcscart`.`cscart_product_prices`.`product_id` in (5,3,2)) and (`_testcscart`.`cscart_product_prices`.`usergroup_id` in (0,1))))"
      }
    }
  }
}