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 (
    431199, 392169, 339707, 430908, 431115, 
    339829, 431133, 339758, 339809, 339769, 
    339677, 339729, 381702, 431050, 431150, 
    339807, 431158, 339648, 431026, 430747, 
    431195, 339479, 430748, 339851, 430681, 
    339712, 339746, 381696, 339847, 430924, 
    431102, 431122, 430907, 339654, 339704, 
    339664, 339735, 430696, 431201, 430648, 
    339760, 339485, 430824, 430916, 387047, 
    430771, 339720, 339817, 430636, 430638, 
    430915, 430998, 431139, 339812, 430646, 
    430857, 431120, 430743, 339835, 430831, 
    430935, 339714, 430803, 430821, 430823, 
    431151, 430813, 381698, 339668, 339715, 
    431145, 387049, 430649, 430665, 430751, 
    381699, 339671, 339820, 431127, 431109, 
    339761, 430647, 339694, 339650, 430848, 
    430766, 339593, 431114, 430660, 430817, 
    339849, 430903, 431097, 431103, 430902, 
    431163, 431194, 339484, 339755, 430818
  ) 
  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 0.00174

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 (431199,392169,339707,430908,431115,339829,431133,339758,339809,339769,339677,339729,381702,431050,431150,339807,431158,339648,431026,430747,431195,339479,430748,339851,430681,339712,339746,381696,339847,430924,431102,431122,430907,339654,339704,339664,339735,430696,431201,430648,339760,339485,430824,430916,387047,430771,339720,339817,430636,430638,430915,430998,431139,339812,430646,430857,431120,430743,339835,430831,430935,339714,430803,430821,430823,431151,430813,381698,339668,339715,431145,387049,430649,430665,430751,381699,339671,339820,431127,431109,339761,430647,339694,339650,430848,430766,339593,431114,430660,430817,339849,430903,431097,431103,430902,431163,431194,339484,339755,430818)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}