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 (
    4241, 3635, 3052, 3634, 3053, 5844, 6034, 
    6035, 6037, 6700, 5896, 5889, 5894, 
    5893, 5897, 5891, 5899, 6096, 6087, 
    6088, 6092, 5883, 5888, 5884, 5885, 
    5886, 5887, 7241, 6743, 1764, 1765, 
    1767, 1763, 3550, 5064, 1672, 1667, 
    1769, 1666, 1669, 4063, 1671, 2986, 
    7213, 7211, 7212, 1513, 1516
  ) 
  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 0.00063

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 (4241,3635,3052,3634,3053,5844,6034,6035,6037,6700,5896,5889,5894,5893,5897,5891,5899,6096,6087,6088,6092,5883,5888,5884,5885,5886,5887,7241,6743,1764,1765,1767,1763,3550,5064,1672,1667,1769,1666,1669,4063,1671,2986,7213,7211,7212,1513,1516))",
        "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)))"
      }
    }
  }
}