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 (
    7676, 7683, 7298, 7297, 5968, 2639, 5113, 
    7295, 7772, 7771, 7294, 7296, 2640, 
    7768, 7759, 7867, 7758, 7868, 2641, 
    7317, 7320, 7321, 2642, 5112, 3141, 
    7318, 3142, 2643, 3143, 7760, 7761, 
    7762, 3144, 5414, 5411, 5413, 5412, 
    5415, 4321, 4320, 4323, 4322, 4324, 
    4325, 4337, 4338, 4340, 4339
  ) 
  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": "39.01"
    },
    "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": 60,
        "rows_produced_per_join": 11,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (7676,7683,7298,7297,5968,2639,5113,7295,7772,7771,7294,7296,2640,7768,7759,7867,7758,7868,2641,7317,7320,7321,2642,5112,3141,7318,3142,2643,3143,7760,7761,7762,3144,5414,5411,5413,5412,5415,4321,4320,4323,4322,4324,4325,4337,4338,4340,4339))",
        "cost_info": {
          "read_cost": "37.86",
          "eval_cost": "1.15",
          "prefix_cost": "39.01",
          "data_read_per_join": "275"
        },
        "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)))"
      }
    }
  }
}