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 (
    13916, 13919, 13929, 13932, 13902, 13931, 
    13939, 13913, 13909, 13924, 13921, 
    13908, 13930, 13938, 13917, 13926, 
    13905, 13906, 13936, 13904, 13933, 
    13912, 13928
  ) 
  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 0.00060

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.059419029,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 46,
          "cost": 0.04473066,
          "filtered": 49.95539856,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (13916,13919,13929,13932,13902,13931,13939,13913,13909,13924,13921,13908,13930,13938,13917,13926,13905,13906,13936,13904,13933,13912,13928) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}