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 (
    4003, 4002, 4006, 4001, 4000, 4598, 2510, 
    2507, 2508, 2511, 2509, 3753, 489, 494, 
    488, 492, 416, 497, 495, 3182, 3181, 
    3656, 1610, 1606, 1608, 491, 1609, 1676, 
    1675, 1607, 1677, 1737, 1736, 100, 95, 
    6430, 6431, 7254, 7255, 4050, 4051, 
    4602, 4049, 4034, 4048, 4419, 4601, 
    4422
  ) 
  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 0.00114

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": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (4003,4002,4006,4001,4000,4598,2510,2507,2508,2511,2509,3753,489,494,488,492,416,497,495,3182,3181,3656,1610,1606,1608,491,1609,1676,1675,1607,1677,1737,1736,100,95,6430,6431,7254,7255,4050,4051,4602,4049,4034,4048,4419,4601,4422))",
        "cost_info": {
          "read_cost": "33.12",
          "eval_cost": "0.94",
          "prefix_cost": "34.06",
          "data_read_per_join": "224"
        },
        "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)))"
      }
    }
  }
}