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 (
    13176, 13162, 13169, 13232, 13225, 13190, 
    13183, 13239, 13204, 13197, 13246, 
    13218, 13211, 13253, 13302, 13303, 
    13308, 13309, 13306, 13307, 13310, 
    13311, 13312, 13313, 13304, 13305, 
    13319, 6962, 6966, 6967, 6965, 6963, 
    6952, 6953, 6947, 6959, 3425, 6958, 
    6960, 6968, 6961, 6964, 6957, 6956, 
    6954, 6955, 6948, 6950, 6949, 13298, 
    13299, 13300, 13301, 13124, 13125, 
    13126, 13098, 13105, 13112, 13118, 
    13064, 13071, 13078, 13085, 13091, 
    13314, 13316, 13315, 13317, 13318, 
    12956, 12958, 13014, 13028, 13040, 
    13052, 12960, 12974, 12988, 13000, 
    12926, 12942
  ) 
  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 0.00208

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "114.81"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 164,
        "rows_produced_per_join": 164,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (13176,13162,13169,13232,13225,13190,13183,13239,13204,13197,13246,13218,13211,13253,13302,13303,13308,13309,13306,13307,13310,13311,13312,13313,13304,13305,13319,6962,6966,6967,6965,6963,6952,6953,6947,6959,3425,6958,6960,6968,6961,6964,6957,6956,6954,6955,6948,6950,6949,13298,13299,13300,13301,13124,13125,13126,13098,13105,13112,13118,13064,13071,13078,13085,13091,13314,13316,13315,13317,13318,12956,12958,13014,13028,13040,13052,12960,12974,12988,13000,12926,12942)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "98.41",
          "eval_cost": "16.40",
          "prefix_cost": "114.81",
          "data_read_per_join": "3K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}