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 (
    431129, 435509, 430656, 430863, 431338, 
    431423, 430856, 430993, 431051, 431074, 
    431165, 339782, 430688, 430702, 430722, 
    430723, 430778, 430816, 430984, 431247, 
    339718, 339675, 431005, 431027, 430627, 
    430742, 430805, 431007, 431022, 431184, 
    339604, 430720, 430839, 430878, 430933, 
    430994, 431177, 430826, 430991, 431019, 
    431357, 430917, 430990, 431108, 431264, 
    431275, 431426, 430872, 430889, 430897, 
    430918, 430940, 431297, 431345, 430690, 
    430791, 430840, 431220, 431501, 430652, 
    430790, 430835, 430958, 430968, 430977, 
    430979, 431342, 430674, 430804, 430828, 
    430886, 430960, 431138, 431358, 430786, 
    430871, 430969, 430931, 430952, 430972, 
    431006, 431428, 431451, 431467, 339597, 
    430780, 431288, 431336, 431395, 430692, 
    430715, 430770, 430894, 430953, 431503, 
    339846, 387050, 430666, 430726, 431037
  ) 
  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 0.00201

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 (431129,435509,430656,430863,431338,431423,430856,430993,431051,431074,431165,339782,430688,430702,430722,430723,430778,430816,430984,431247,339718,339675,431005,431027,430627,430742,430805,431007,431022,431184,339604,430720,430839,430878,430933,430994,431177,430826,430991,431019,431357,430917,430990,431108,431264,431275,431426,430872,430889,430897,430918,430940,431297,431345,430690,430791,430840,431220,431501,430652,430790,430835,430958,430968,430977,430979,431342,430674,430804,430828,430886,430960,431138,431358,430786,430871,430969,430931,430952,430972,431006,431428,431451,431467,339597,430780,431288,431336,431395,430692,430715,430770,430894,430953,431503,339846,387050,430666,430726,431037)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}