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 (
    12916, 12921, 12956, 12958, 13014, 13028, 
    13040, 13052, 12960, 12974, 12988, 
    13000, 13148, 13153, 12928, 12926, 
    12942, 3135, 12850, 12869, 12876, 12896, 
    12900, 12909, 12752, 12802, 3403, 3404, 
    3405, 3406, 3408, 3409, 6930, 6931, 
    6932, 6933, 6934, 6935, 6936, 3407, 
    2666, 3845, 12796, 12797, 2667, 2668, 
    2669, 2670
  ) 
  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 0.00185

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.21"
    },
    "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": 96,
        "rows_produced_per_join": 96,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (12916,12921,12956,12958,13014,13028,13040,13052,12960,12974,12988,13000,13148,13153,12928,12926,12942,3135,12850,12869,12876,12896,12900,12909,12752,12802,3403,3404,3405,3406,3408,3409,6930,6931,6932,6933,6934,6935,6936,3407,2666,3845,12796,12797,2667,2668,2669,2670)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "57.61",
          "eval_cost": "9.60",
          "prefix_cost": "67.21",
          "data_read_per_join": "2K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}