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 (
    3095, 3101, 3108, 6683, 6697, 3099, 19, 
    20, 21, 3929, 3930, 3931, 3414, 6938, 
    6941, 6944, 3412, 6937, 6939, 6943, 
    6724, 3100, 3106, 3114, 3120, 3125, 
    3153, 3154, 6672, 6688, 6689, 6694, 
    6702, 6706, 6708, 6726, 6725, 3103, 
    3097, 3113, 6687, 6699, 36, 37, 38, 39, 
    40, 41
  ) 
  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 0.00102

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 (3095,3101,3108,6683,6697,3099,19,20,21,3929,3930,3931,3414,6938,6941,6944,3412,6937,6939,6943,6724,3100,3106,3114,3120,3125,3153,3154,6672,6688,6689,6694,6702,6706,6708,6726,6725,3103,3097,3113,6687,6699,36,37,38,39,40,41))",
        "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)))"
      }
    }
  }
}