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 (
    2803, 3568, 5715, 5716, 17265, 3868, 
    41340, 3567, 3869, 5717, 5990, 47655, 
    27359, 5789, 34555, 47922, 47921, 41343, 
    47896, 47924, 31638, 3870, 114, 47923, 
    1582, 33312, 31633, 31632, 3287, 3286, 
    3872, 113
  ) 
  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 0.00342

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 (2803,3568,5715,5716,17265,3868,41340,3567,3869,5717,5990,47655,27359,5789,34555,47922,47921,41343,47896,47924,31638,3870,114,47923,1582,33312,31633,31632,3287,3286,3872,113)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}