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 (
    350338, 352750, 353135, 353755, 358653, 
    350063, 350891, 353573, 354233, 354557, 
    355013, 357118, 357303, 358590, 351072, 
    351228, 352097, 352904, 352962, 354288, 
    356454, 350162, 351229, 351544, 351553, 
    354141, 356403, 357959, 350158, 350234, 
    350694, 350791, 350930, 353432, 354069, 
    355749, 357856, 359081, 350581, 350754, 
    352145, 353373, 356087, 358897, 352105, 
    355630, 356847, 356938, 357320, 358940, 
    350072, 352018, 352381, 353444, 354005, 
    354119, 355550, 349950, 351063, 351145, 
    356295, 356513, 358952, 351062, 352101, 
    352686, 354643, 356626, 356637, 359095, 
    350636, 353246, 353445, 356188, 356931, 
    357166, 357702, 349961, 352824, 354391, 
    355180, 357066, 350340, 350494, 351100, 
    353419, 355235, 357310, 357415, 349868, 
    351452, 352935, 353340, 355823, 355895, 
    356920, 356966, 349849, 350265, 350512
  ) 
  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 0.00250

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "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": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (350338,352750,353135,353755,358653,350063,350891,353573,354233,354557,355013,357118,357303,358590,351072,351228,352097,352904,352962,354288,356454,350162,351229,351544,351553,354141,356403,357959,350158,350234,350694,350791,350930,353432,354069,355749,357856,359081,350581,350754,352145,353373,356087,358897,352105,355630,356847,356938,357320,358940,350072,352018,352381,353444,354005,354119,355550,349950,351063,351145,356295,356513,358952,351062,352101,352686,354643,356626,356637,359095,350636,353246,353445,356188,356931,357166,357702,349961,352824,354391,355180,357066,350340,350494,351100,353419,355235,357310,357415,349868,351452,352935,353340,355823,355895,356920,356966,349849,350265,350512)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}