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 (
    1061, 38129, 41407, 1174, 1062, 5578, 
    5759, 1745, 3639, 5636, 2295, 5579, 
    23481, 6660, 16847, 49018, 5478, 3768, 
    48847, 2083, 5405, 4595, 5580, 3989, 
    1768, 40309, 4597, 47652, 2086, 5770, 
    41418, 798
  ) 
  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 0.00626

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 (1061,38129,41407,1174,1062,5578,5759,1745,3639,5636,2295,5579,23481,6660,16847,49018,5478,3768,48847,2083,5405,4595,5580,3989,1768,40309,4597,47652,2086,5770,41418,798)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}