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 (
    6536, 21063, 1784, 6545, 1747, 1056, 
    79, 5765, 1711, 585, 1749, 48850, 23172, 
    40811, 4271, 1756, 5769, 24798, 6543, 
    40808, 4272, 5772, 14982, 5759, 1745, 
    4939, 2128, 1748, 23481, 6467, 48847, 
    1751
  ) 
  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 0.00793

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 (6536,21063,1784,6545,1747,1056,79,5765,1711,585,1749,48850,23172,40811,4271,1756,5769,24798,6543,40808,4272,5772,14982,5759,1745,4939,2128,1748,23481,6467,48847,1751)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}