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 (
    339484, 339755, 430807, 431068, 339697, 
    431359, 430875, 431041, 430825, 430868, 
    431085, 431156, 339681, 339828, 430925, 
    431053, 431164, 381705, 430819, 430820, 
    430901, 431013, 431049, 339596, 430654, 
    430658, 431144, 431148, 430691, 430989, 
    430746, 430808, 430812, 430834, 430629, 
    430680, 431136, 339774, 339765, 430843, 
    339728, 339836, 339843, 431110, 339725, 
    339734, 339816, 431080, 339655, 339839, 
    339599, 431118, 431161, 339466, 430673, 
    430890, 339845, 430789, 430859, 430906, 
    430922, 339582, 339723, 431082, 431126, 
    430657, 430678, 339702, 430737, 430822, 
    430860, 431111, 339674, 430689, 431044, 
    339754, 381704, 430795, 430832, 430892, 
    430914, 430921, 430635, 339802, 339821, 
    430663, 430838, 430854, 431174, 339486, 
    430650, 430959, 431456, 430815, 339727, 
    381697, 431169, 430672, 430695, 430950
  ) 
  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 0.00153

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 (339484,339755,430807,431068,339697,431359,430875,431041,430825,430868,431085,431156,339681,339828,430925,431053,431164,381705,430819,430820,430901,431013,431049,339596,430654,430658,431144,431148,430691,430989,430746,430808,430812,430834,430629,430680,431136,339774,339765,430843,339728,339836,339843,431110,339725,339734,339816,431080,339655,339839,339599,431118,431161,339466,430673,430890,339845,430789,430859,430906,430922,339582,339723,431082,431126,430657,430678,339702,430737,430822,430860,431111,339674,430689,431044,339754,381704,430795,430832,430892,430914,430921,430635,339802,339821,430663,430838,430854,431174,339486,430650,430959,431456,430815,339727,381697,431169,430672,430695,430950)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}