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 (
    49012, 6370, 3288, 49164, 47903, 49230, 
    28159, 43817, 48846, 1894, 23152, 47631, 
    1533, 6372, 49873, 6358, 6357, 41345, 
    41341, 35279, 25318, 47597, 47084, 
    5787, 1767, 3866, 5503, 18608, 2140, 
    2139, 5987, 42255
  ) 
  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 0.00403

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 (49012,6370,3288,49164,47903,49230,28159,43817,48846,1894,23152,47631,1533,6372,49873,6358,6357,41345,41341,35279,25318,47597,47084,5787,1767,3866,5503,18608,2140,2139,5987,42255)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}