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 (
    309474, 309478, 206988, 391625, 309476, 
    391630, 309469, 391627, 391629, 262380, 
    309470, 252156, 206990, 206986, 309475, 
    309431, 391628, 206991, 309472, 252154, 
    391631, 339432, 265269, 206468, 339433, 
    262428, 308644, 206965, 13481, 13466, 
    339434, 339438, 262429, 206983, 308657, 
    206950, 262440, 262370, 262437, 206929, 
    308646, 339439, 230172, 259698, 13488, 
    206977, 339445, 13474, 262430, 252155, 
    262436, 262434, 262432, 13486, 339440, 
    206993, 262441, 173883, 13468, 262400, 
    230173, 339511, 339515, 206933, 339441, 
    13469, 254299, 13485, 252159, 13484, 
    254297, 252157, 427782, 253161, 262359, 
    225088, 262438, 253198, 262435, 253157, 
    262439, 81573, 81586, 225081, 225074, 
    35390, 254305, 159862, 38238, 13487, 
    225053, 262399, 262394, 252161, 225066, 
    262442, 252162, 287, 81610, 286682
  ) 
  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 0.00178

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 (309474,309478,206988,391625,309476,391630,309469,391627,391629,262380,309470,252156,206990,206986,309475,309431,391628,206991,309472,252154,391631,339432,265269,206468,339433,262428,308644,206965,13481,13466,339434,339438,262429,206983,308657,206950,262440,262370,262437,206929,308646,339439,230172,259698,13488,206977,339445,13474,262430,252155,262436,262434,262432,13486,339440,206993,262441,173883,13468,262400,230173,339511,339515,206933,339441,13469,254299,13485,252159,13484,254297,252157,427782,253161,262359,225088,262438,253198,262435,253157,262439,81573,81586,225081,225074,35390,254305,159862,38238,13487,225053,262399,262394,252161,225066,262442,252162,287,81610,286682)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}