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 (
    431456, 339702, 387049, 339593, 430751, 
    431148, 430660, 430825, 431127, 430680, 
    430691, 430820, 431013, 430678, 339849, 
    430875, 430959, 431194, 431035, 431041, 
    431044, 431049, 431109, 339483, 339484, 
    431083, 339820, 430737, 430756, 430989, 
    431080, 431161, 430635, 339734, 381698, 
    381699, 430650, 430922, 430808, 430819, 
    430843, 430629, 430657, 430807, 339596, 
    430868, 430921, 431126, 431144, 430795, 
    430928, 431073, 431082, 430789, 430812, 
    430950, 339725, 430658, 430758, 430901, 
    431110, 339674, 430818, 431156, 339774, 
    339728, 339754, 430673, 430689, 430822, 
    430860, 431114, 339821, 339836, 430684, 
    430664, 430769, 430892, 431043, 431066, 
    431169, 339466, 381705, 430842, 430628, 
    430834, 431064, 339843, 339802, 430859, 
    431459, 430906, 381697, 430768, 430890, 
    430962, 431118, 431250, 430703, 430988
  ) 
  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 0.00160

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 (431456,339702,387049,339593,430751,431148,430660,430825,431127,430680,430691,430820,431013,430678,339849,430875,430959,431194,431035,431041,431044,431049,431109,339483,339484,431083,339820,430737,430756,430989,431080,431161,430635,339734,381698,381699,430650,430922,430808,430819,430843,430629,430657,430807,339596,430868,430921,431126,431144,430795,430928,431073,431082,430789,430812,430950,339725,430658,430758,430901,431110,339674,430818,431156,339774,339728,339754,430673,430689,430822,430860,431114,339821,339836,430684,430664,430769,430892,431043,431066,431169,339466,381705,430842,430628,430834,431064,339843,339802,430859,431459,430906,381697,430768,430890,430962,431118,431250,430703,430988)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}