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 (
    6606, 6607, 6608, 6610, 6611, 6612, 6613, 
    3024, 3025, 3026, 3027, 3301, 6847, 
    3300, 2841, 2842, 2843, 2844, 6426, 
    6427, 6428, 6429, 6430, 2765, 2766, 
    2767, 2768, 6352, 6353, 6354, 6355, 
    6356, 2185, 2186, 2187, 2188, 5785, 
    5786, 5787, 5788, 5789, 6641, 6219, 
    5807, 3722, 5819, 1516, 6623
  ) 
  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 0.00147

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (6606,6607,6608,6610,6611,6612,6613,3024,3025,3026,3027,3301,6847,3300,2841,2842,2843,2844,6426,6427,6428,6429,6430,2765,2766,2767,2768,6352,6353,6354,6355,6356,2185,2186,2187,2188,5785,5786,5787,5788,5789,6641,6219,5807,3722,5819,1516,6623))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}