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 (
    51514, 51538, 51539, 51468, 51476, 51491, 
    51513, 51474, 51503, 51520, 51541, 
    51462, 51502, 51522, 51499, 51465, 
    51509, 51515, 51466, 51485, 51518, 
    51550, 51519, 51524, 51528, 51508, 
    51527, 51543, 51482, 51504, 51542, 
    51512, 51493, 51511, 51505, 51046, 
    51439, 51544, 51054, 51546, 51548, 
    51438, 51535
  ) 
  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 0.00111

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.16"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 52,
        "rows_produced_per_join": 10,
        "filtered": "19.96",
        "index_condition": "(`test_uchur_k`.`cscart_product_prices`.`product_id` in (51514,51538,51539,51468,51476,51491,51513,51474,51503,51520,51541,51462,51502,51522,51499,51465,51509,51515,51466,51485,51518,51550,51519,51524,51528,51508,51527,51543,51482,51504,51542,51512,51493,51511,51505,51046,51439,51544,51054,51546,51548,51438,51535))",
        "cost_info": {
          "read_cost": "33.12",
          "eval_cost": "1.04",
          "prefix_cost": "34.16",
          "data_read_per_join": "249"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test_uchur_k`.`cscart_product_prices`.`lower_limit` = 1) and (`test_uchur_k`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}