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 (
    3587, 5549, 34671, 27863, 2964, 31640, 
    40440, 3586, 45507, 389, 1713, 44422, 
    2278, 3874, 2514, 2287, 5569, 46751, 
    6059, 48769, 31630, 6060, 4440, 18258, 
    14822, 18201, 2461, 31909, 31908, 2505, 
    4441, 6099
  ) 
  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 0.01002

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (3587,5549,34671,27863,2964,31640,40440,3586,45507,389,1713,44422,2278,3874,2514,2287,5569,46751,6059,48769,31630,6060,4440,18258,14822,18201,2461,31909,31908,2505,4441,6099)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}