SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    154, 53, 52, 228, 161, 165, 166, 86, 106, 
    105, 247, 101, 33, 32, 163, 244, 212, 
    155, 55, 69, 206, 184, 183, 133, 132, 
    125, 120, 223, 225, 224, 146, 147, 145, 
    117, 219, 222, 220, 221, 113, 157, 68, 
    29, 6, 8, 14, 9, 10, 19, 21, 50, 51, 49, 
    48, 54, 153, 164, 248, 65, 64, 63, 62, 
    66, 140, 141
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00164

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "60.00"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "table": {
        "table_name": "cscart_ult_product_prices",
        "access_type": "ref",
        "possible_keys": [
          "usergroup",
          "product_id",
          "company_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "company_id",
        "used_key_parts": [
          "company_id"
        ],
        "key_length": "4",
        "ref": [
          "const"
        ],
        "rows_examined_per_scan": 240,
        "rows_produced_per_join": 16,
        "filtered": "6.96",
        "index_condition": "(`rajansecarter_single_store_19_jan`.`cscart_ult_product_prices`.`company_id` <=> 1)",
        "cost_info": {
          "read_cost": "12.00",
          "eval_cost": "3.34",
          "prefix_cost": "60.00",
          "data_read_per_join": "534"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "company_id",
          "usergroup_id"
        ],
        "attached_condition": "((`rajansecarter_single_store_19_jan`.`cscart_ult_product_prices`.`lower_limit` = 1) and (`rajansecarter_single_store_19_jan`.`cscart_ult_product_prices`.`product_id` in (154,53,52,228,161,165,166,86,106,105,247,101,33,32,163,244,212,155,55,69,206,184,183,133,132,125,120,223,225,224,146,147,145,117,219,222,220,221,113,157,68,29,6,8,14,9,10,19,21,50,51,49,48,54,153,164,248,65,64,63,62,66,140,141)) and (`rajansecarter_single_store_19_jan`.`cscart_ult_product_prices`.`usergroup_id` in (0,0,1)))"
      }
    }
  }
}