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 (
    1040, 2086, 36476, 3981, 5800, 4433, 
    36469, 3982, 4383, 979, 978, 5635, 5381, 
    36466, 2259, 15235, 4003, 6519, 5799, 
    2248, 5420, 41445, 40725, 3996, 3237, 
    36303, 38151, 2256, 35193, 982, 4384, 
    36302
  ) 
  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 0.00700

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 (1040,2086,36476,3981,5800,4433,36469,3982,4383,979,978,5635,5381,36466,2259,15235,4003,6519,5799,2248,5420,41445,40725,3996,3237,36303,38151,2256,35193,982,4384,36302)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}