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 (
    430926, 430940, 431264, 431301, 431339, 
    431426, 435509, 430782, 430879, 431020, 
    431022, 431193, 430816, 431275, 339726, 
    430661, 430794, 431171, 430641, 430788, 
    430811, 430839, 431334, 339825, 430675, 
    430742, 430863, 430968, 431055, 430953, 
    431428, 430805, 430894, 431005, 431098, 
    431244, 339855, 339718, 430688, 430755, 
    430800, 430826, 430917, 430952, 430979, 
    431006, 431262, 430713, 430874, 431028, 
    431336, 431504, 430778, 430827, 430852, 
    430855, 430856, 430931, 430991, 431000, 
    431027, 431101, 431451, 431177, 431184, 
    431358, 430864, 431469, 430694, 430780, 
    431234, 431368, 339675, 430671, 430918, 
    430995, 431342, 430897, 431420, 430702, 
    430706, 430840, 430878, 430888, 430977, 
    430990, 431357, 339597, 430666, 431010, 
    431344, 430667, 430871, 431297, 431381, 
    339782, 381709, 430692, 430997, 431025
  ) 
  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 0.00116

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 (430926,430940,431264,431301,431339,431426,435509,430782,430879,431020,431022,431193,430816,431275,339726,430661,430794,431171,430641,430788,430811,430839,431334,339825,430675,430742,430863,430968,431055,430953,431428,430805,430894,431005,431098,431244,339855,339718,430688,430755,430800,430826,430917,430952,430979,431006,431262,430713,430874,431028,431336,431504,430778,430827,430852,430855,430856,430931,430991,431000,431027,431101,431451,431177,431184,431358,430864,431469,430694,430780,431234,431368,339675,430671,430918,430995,431342,430897,431420,430702,430706,430840,430878,430888,430977,430990,431357,339597,430666,431010,431344,430667,430871,431297,431381,339782,381709,430692,430997,431025)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}