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 (
    621, 860, 619, 861, 5653, 59, 122, 5662, 
    61, 2992, 5663, 123, 63, 58, 121, 124, 
    62, 785, 784, 786, 782, 787, 783, 1511, 
    3586, 1924, 1773, 3665, 3666, 4625, 
    6421, 7262, 5971, 1727, 5957, 6422, 
    6423, 6424, 7252, 7253, 7250, 6717, 
    6719, 6718, 7251, 4614, 3869, 1772
  ) 
  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 0.00102

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (621,860,619,861,5653,59,122,5662,61,2992,5663,123,63,58,121,124,62,785,784,786,782,787,783,1511,3586,1924,1773,3665,3666,4625,6421,7262,5971,1727,5957,6422,6423,6424,7252,7253,7250,6717,6719,6718,7251,4614,3869,1772))",
        "cost_info": {
          "read_cost": "32.69",
          "eval_cost": "0.92",
          "prefix_cost": "33.61",
          "data_read_per_join": "220"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`dbggbern`.`cscart_product_prices`.`lower_limit` = 1) and (`dbggbern`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}