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 (
    3751, 3758, 3759, 3762, 47563, 3748, 
    4042, 4596, 4656, 4646, 3766, 4623, 
    3761, 4039, 3763, 6513, 6260, 4598, 
    4640, 46714, 4632, 47280, 6403, 6259, 
    48062, 6258, 4603, 6257, 47197, 47855, 
    47367, 4635
  ) 
  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 0.00654

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 (3751,3758,3759,3762,47563,3748,4042,4596,4656,4646,3766,4623,3761,4039,3763,6513,6260,4598,4640,46714,4632,47280,6403,6259,48062,6258,4603,6257,47197,47855,47367,4635)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}