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 (
    3612, 3613, 3614, 3615, 4224, 4225, 4226, 
    4227, 4228, 4229, 4230, 5079, 5080, 
    5081, 5082, 5083, 5084, 5085, 5086, 
    5087, 5088, 5089, 5090, 5091, 5092, 
    5093, 5094, 5095, 5096, 5097, 5098, 
    5099, 5100, 5101, 5102, 5103, 5104, 
    5105, 5106, 2760, 2761, 2762, 2763, 
    2764, 6348, 6349, 6350, 6351
  ) 
  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": "34.06"
    },
    "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": 49,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (3612,3613,3614,3615,4224,4225,4226,4227,4228,4229,4230,5079,5080,5081,5082,5083,5084,5085,5086,5087,5088,5089,5090,5091,5092,5093,5094,5095,5096,5097,5098,5099,5100,5101,5102,5103,5104,5105,5106,2760,2761,2762,2763,2764,6348,6349,6350,6351))",
        "cost_info": {
          "read_cost": "33.08",
          "eval_cost": "0.98",
          "prefix_cost": "34.06",
          "data_read_per_join": "235"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}