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 (
    687122, 480529, 1133394, 1108257, 1114057, 
    612918, 431479, 1108259, 1108324, 
    1108375, 1192887, 1108255, 698147, 
    1005477, 1005469, 600012, 696950, 
    695183, 621062, 620876, 697432, 621045, 
    620921, 620902, 600132, 697717, 600044, 
    614824, 621019, 600112, 697903, 992455, 
    600286, 991897, 621108, 1000097, 1083988, 
    999893, 1006365, 1123986, 1282930, 
    1108822, 1158435, 1108819, 1108820, 
    1153203, 1282939, 1283561, 1283295, 
    1283299, 1129290, 1590985, 1228395, 
    1707787, 1181767, 1167142
  ) 
  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 0.00204

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "1.20"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": false,
      "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": 7,
        "rows_produced_per_join": 1,
        "filtered": "27.00",
        "cost_info": {
          "read_cost": "0.50",
          "eval_cost": "0.19",
          "prefix_cost": "1.20",
          "data_read_per_join": "60"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "company_id",
          "usergroup_id"
        ],
        "attached_condition": "((`maniamall_cscart`.`cscart_ult_product_prices`.`lower_limit` = 1) and (`maniamall_cscart`.`cscart_ult_product_prices`.`product_id` in (687122,480529,1133394,1108257,1114057,612918,431479,1108259,1108324,1108375,1192887,1108255,698147,1005477,1005469,600012,696950,695183,621062,620876,697432,621045,620921,620902,600132,697717,600044,614824,621019,600112,697903,992455,600286,991897,621108,1000097,1083988,999893,1006365,1123986,1282930,1108822,1158435,1108819,1108820,1153203,1282939,1283561,1283295,1283299,1129290,1590985,1228395,1707787,1181767,1167142)) and (`maniamall_cscart`.`cscart_ult_product_prices`.`usergroup_id` in (0,0,1)))"
      }
    }
  }
}