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, 6128, 2181, 29737, 41774, 1532, 
    40760, 6159, 46143, 40759, 26919, 6172, 
    41600, 6125, 26925, 46141, 6169, 14950, 
    26928, 3495, 6095, 1473, 26926, 47899, 
    6164, 26923, 6171, 26921, 6127, 6170, 
    6541, 26929
  ) 
  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 0.00486

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 (6536,6128,2181,29737,41774,1532,40760,6159,46143,40759,26919,6172,41600,6125,26925,46141,6169,14950,26928,3495,6095,1473,26926,47899,6164,26923,6171,26921,6127,6170,6541,26929)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}