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 (
    6126, 61, 62, 41831, 6539, 6162, 6163, 
    26930, 6168, 26931, 6167, 47905, 47164, 
    31666, 6160, 47900, 6166, 29740, 29738, 
    26967, 44761, 26932, 26866, 47901, 
    6161, 29742, 29741, 6096, 28243, 28244, 
    43663, 6190
  ) 
  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 0.00447

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 (6126,61,62,41831,6539,6162,6163,26930,6168,26931,6167,47905,47164,31666,6160,47900,6166,29740,29738,26967,44761,26932,26866,47901,6161,29742,29741,6096,28243,28244,43663,6190)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}