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 (
    4002, 4003, 4004, 4005, 4059, 4060, 4061, 
    4062, 4063, 4064, 4065, 4142, 4143, 
    4144, 4145, 4146, 4147, 4148, 4195, 
    4196, 4197, 4198, 4199, 4200, 4201, 
    6716, 6715, 3117, 3119, 3127, 3133, 
    3141, 3142, 6674, 6680, 6692, 6693, 
    6701, 6707, 1417, 1393, 1394, 1395, 
    1396, 1397, 1398, 1399, 1400
  ) 
  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 0.00098

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 (4002,4003,4004,4005,4059,4060,4061,4062,4063,4064,4065,4142,4143,4144,4145,4146,4147,4148,4195,4196,4197,4198,4199,4200,4201,6716,6715,3117,3119,3127,3133,3141,3142,6674,6680,6692,6693,6701,6707,1417,1393,1394,1395,1396,1397,1398,1399,1400))",
        "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)))"
      }
    }
  }
}