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 (
    5589, 5447, 4365, 31886, 5469, 4468, 
    4358, 5464, 5474, 5962, 4464, 4364, 
    4466, 31897, 47280, 4359, 5481, 5459, 
    31896, 48032, 4357, 48322, 31892, 31890, 
    4467, 47088, 31898, 5483, 47090, 48033, 
    48030, 48037
  ) 
  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 0.00535

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 (5589,5447,4365,31886,5469,4468,4358,5464,5474,5962,4464,4364,4466,31897,47280,4359,5481,5459,31896,48032,4357,48322,31892,31890,4467,47088,31898,5483,47090,48033,48030,48037)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}