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 (
    3470, 1710, 5568, 2237, 6533, 3469, 46739, 
    46734, 16601, 1781, 6466, 2138, 35734, 
    48843, 1755, 16612, 1754, 2131, 6468, 
    6529, 2130, 40455, 27350, 6534, 2137, 
    6535, 5815, 21600, 2129, 1712, 1750, 
    48844
  ) 
  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 0.00210

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 (3470,1710,5568,2237,6533,3469,46739,46734,16601,1781,6466,2138,35734,48843,1755,16612,1754,2131,6468,6529,2130,40455,27350,6534,2137,6535,5815,21600,2129,1712,1750,48844)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}