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 (
    10489, 10471, 9880, 10472, 9885, 10488, 
    9897, 9895, 10467, 9900, 10470, 10466, 
    10477, 9889, 10475, 9890, 10483, 10495, 
    10490, 10469, 9877, 9894, 9891, 10480, 
    9893, 9878, 9886, 9882, 9888, 10482, 
    13091, 12551, 12638, 12634, 12636, 
    12635, 12599, 12627, 12600, 12639, 
    15800, 12595, 12587, 12593, 12620, 
    12623, 12619, 12585, 12616, 12601, 
    12628, 12602, 12640, 12647, 12588, 
    12605, 12606, 12637, 12612, 12613, 
    12641, 12554, 12552, 12642
  ) 
  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 0.00102

JSON explain

{
  "query_block": {
    "select_id": 1,
    "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": 64,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (10489,10471,9880,10472,9885,10488,9897,9895,10467,9900,10470,10466,10477,9889,10475,9890,10483,10495,10490,10469,9877,9894,9891,10480,9893,9878,9886,9882,9888,10482,13091,12551,12638,12634,12636,12635,12599,12627,12600,12639,15800,12595,12587,12593,12620,12623,12619,12585,12616,12601,12628,12602,12640,12647,12588,12605,12606,12637,12612,12613,12641,12554,12552,12642)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9877 1036.29000000
9878 1036.29000000
9880 1036.29000000
9882 1036.29000000
9885 1036.29000000
9886 1036.29000000
9888 1036.29000000
9889 1036.29000000
9890 1036.29000000
9891 1036.29000000
9893 1036.29000000
9894 1036.29000000
9895 1036.29000000
9897 1036.29000000
9900 1036.29000000
10466 1036.29000000
10467 1036.29000000
10469 1036.29000000
10470 1036.29000000
10471 1036.29000000
10472 1036.29000000
10475 1036.29000000
10477 1036.29000000
10480 1036.29000000
10482 1036.29000000
10483 1036.29000000
10488 1036.29000000
10489 1036.29000000
10490 1036.29000000
10495 1036.29000000
12551 15215.00000000
12552 14984.00000000
12554 19331.00000000
12585 209523.67000000
12587 209523.67000000
12588 6750.00000000
12593 349146.47000000
12595 131354.16000000
12599 14092.68000000
12600 4597.28000000
12601 14092.68000000
12602 4597.28000000
12605 14092.68000000
12606 4597.28000000
12612 15852.84000000
12613 15852.84000000
12616 15852.84000000
12619 131354.16000000
12620 131354.16000000
12623 209523.67000000
12627 21943.06000000
12628 21943.06000000
12634 25398.80000000
12635 25398.80000000
12636 46725.90000000
12637 19650.51000000
12638 19593.76000000
12639 19593.76000000
12640 19593.76000000
12641 19593.76000000
12642 19593.76000000
12647 33378.35000000
13091 6750.00000000
15800 33378.35000000