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 (
    4116, 4136, 4115, 4127, 4087, 4126, 4086, 
    4128, 4089, 4091, 4108, 4085, 4090, 
    4971
  ) 
  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 0.00036

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_ult_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_ult_product_prices",
          "access_type": "ALL",
          "possible_keys": [
            "usergroup",
            "product_id",
            "company_id",
            "lower_limit",
            "usergroup_id"
          ],
          "rows": 44,
          "filtered": 31.81818199,
          "attached_condition": "cscart_ult_product_prices.lower_limit = 1 and cscart_ult_product_prices.company_id = 1 and cscart_ult_product_prices.product_id in (4116,4136,4115,4127,4087,4126,4086,4128,4089,4091,4108,4085,4090,4971) and cscart_ult_product_prices.usergroup_id in (0,0,1)"
        }
      }
    }
  }
}