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 (
    51480, 51479, 51494, 51495, 132, 112, 
    3, 78, 2, 77, 87, 66, 22421, 22424, 22290, 
    50981, 50982, 133, 45, 143, 50983, 51416, 
    51043, 51421, 51471, 51413, 51057, 
    51472, 51547, 51470, 51500, 51412, 
    51529, 51459, 51457, 51460, 51501, 
    51530, 51464, 51051, 51053, 51551, 
    51478, 51469, 51510, 51486, 51531, 
    51467, 51047, 51461, 51044, 51475, 
    51477, 51473, 51437, 51540, 51048, 
    51525, 51458, 51463, 51516, 51532, 
    51545, 51492
  ) 
  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 0.00106

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "49.76"
    },
    "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": 75,
        "rows_produced_per_join": 14,
        "filtered": "19.96",
        "index_condition": "(`test_uchur_k`.`cscart_product_prices`.`product_id` in (51480,51479,51494,51495,132,112,3,78,2,77,87,66,22421,22424,22290,50981,50982,133,45,143,50983,51416,51043,51421,51471,51413,51057,51472,51547,51470,51500,51412,51529,51459,51457,51460,51501,51530,51464,51051,51053,51551,51478,51469,51510,51486,51531,51467,51047,51461,51044,51475,51477,51473,51437,51540,51048,51525,51458,51463,51516,51532,51545,51492))",
        "cost_info": {
          "read_cost": "48.26",
          "eval_cost": "1.50",
          "prefix_cost": "49.76",
          "data_read_per_join": "359"
        },
        "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)))"
      }
    }
  }
}