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 (
    47984, 36329, 3884, 5411, 40761, 41421, 
    40452, 38558, 1123, 6211, 3471, 3781, 
    39613, 40454, 47660, 40453, 3859, 3789, 
    2917, 2906, 3860, 6089, 14965, 6562, 
    1781, 3883, 48770, 48843, 775, 1755, 
    6212, 3620
  ) 
  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 0.00297

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 (47984,36329,3884,5411,40761,41421,40452,38558,1123,6211,3471,3781,39613,40454,47660,40453,3859,3789,2917,2906,3860,6089,14965,6562,1781,3883,48770,48843,775,1755,6212,3620)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}