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 (
    5546, 48769, 31630, 37304, 5556, 16607, 
    6060, 2920, 38143, 4440, 5837, 27357, 
    38152, 35249, 27358, 2932, 18258, 46735, 
    14822, 18201, 40824, 2461, 41441, 31909, 
    5554, 31908, 2505, 4441, 6099, 5779, 
    34672, 33177
  ) 
  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 0.02215

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 (5546,48769,31630,37304,5556,16607,6060,2920,38143,4440,5837,27357,38152,35249,27358,2932,18258,46735,14822,18201,40824,2461,41441,31909,5554,31908,2505,4441,6099,5779,34672,33177)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}