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 (
    4070, 4154, 4144, 4152, 4153, 4029, 4026, 
    3999, 4003, 4005, 4155, 4156, 4157, 
    4158, 4159, 4160, 4114, 4112, 4204, 
    4208, 4209, 4210, 4110, 4111, 4130, 
    4132, 4133, 4134, 3977, 4055
  ) 
  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 0.00778

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 6449,
          "filtered": 4.305534363,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (4070,4154,4144,4152,4153,4029,4026,3999,4003,4005,4155,4156,4157,4158,4159,4160,4114,4112,4204,4208,4209,4210,4110,4111,4130,4132,4133,4134,3977,4055) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}