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 (
    9984, 
    9985, 
    9986, 
    9987, 
    9988, 
    9989, 
    9990, 
    9991, 
    9992, 
    9993, 
    9994, 
    9995, 
    9996, 
    9997, 
    9998, 
    9999, 
    12995, 
    12996, 
    12997, 
    12998, 
    10734, 
    10735, 
    10736, 
    10737, 
    10738, 
    10747, 
    10748, 
    10749, 
    10750, 
    10751, 
    10752, 
    15744, 
    15745, 
    15746, 
    15743, 
    15738, 
    15739, 
    15740, 
    15741, 
    15742, 
    15736, 
    15737, 
    10668, 
    10669, 
    10670, 
    10671, 
    10672, 
    10673, 
    10674, 
    10675, 
    10676, 
    10677, 
    10678, 
    10679, 
    10680, 
    10681, 
    10682, 
    10683, 
    10684, 
    10685, 
    10686, 
    10607, 
    10608, 
    10609, 
    10610, 
    10611, 
    10612, 
    10613, 
    10614, 
    10615, 
    10616, 
    10617, 
    10618, 
    10619, 
    10620, 
    10621, 
    10622, 
    10623, 
    10624, 
    9685, 
    10653, 
    10646, 
    10645, 
    10647, 
    10648, 
    10649, 
    10726, 
    10650, 
    10547, 
    9789, 
    10655, 
    10654, 
    10605, 
    10604, 
    9873, 
    9972, 
    9973, 
    9975, 
    9976, 
    9977, 
    9978, 
    9979, 
    10179, 
    10180, 
    10523, 
    10073, 
    10077, 
    10076, 
    10086, 
    10085, 
    10084, 
    10083, 
    10082, 
    10081, 
    10080, 
    10079, 
    10584, 
    10594, 
    9814, 
    9815, 
    9816, 
    9817, 
    9818, 
    15732, 
    9820, 
    9821, 
    9822, 
    9823
  ) 
  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 0.00237

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": 128,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (9984,9985,9986,9987,9988,9989,9990,9991,9992,9993,9994,9995,9996,9997,9998,9999,12995,12996,12997,12998,10734,10735,10736,10737,10738,10747,10748,10749,10750,10751,10752,15744,15745,15746,15743,15738,15739,15740,15741,15742,15736,15737,10668,10669,10670,10671,10672,10673,10674,10675,10676,10677,10678,10679,10680,10681,10682,10683,10684,10685,10686,10607,10608,10609,10610,10611,10612,10613,10614,10615,10616,10617,10618,10619,10620,10621,10622,10623,10624,9685,10653,10646,10645,10647,10648,10649,10726,10650,10547,9789,10655,10654,10605,10604,9873,9972,9973,9975,9976,9977,9978,9979,10179,10180,10523,10073,10077,10076,10086,10085,10084,10083,10082,10081,10080,10079,10584,10594,9814,9815,9816,9817,9818,15732,9820,9821,9822,9823)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9685 4000.00000000
9789 1381.72000000
9814 1136.58000000
9815 1136.58000000
9816 1136.58000000
9817 1136.58000000
9818 1136.58000000
9820 1136.58000000
9821 1136.58000000
9822 1136.58000000
9823 1136.58000000
9873 2997.44000000
9972 582.40000000
9973 582.40000000
9975 582.40000000
9976 582.40000000
9977 582.40000000
9978 582.40000000
9979 582.40000000
9984 1241.41000000
9985 1241.41000000
9986 1241.41000000
9987 1241.41000000
9988 1241.41000000
9989 1241.41000000
9990 1241.41000000
9991 1241.41000000
9992 1241.41000000
9993 1241.41000000
9994 1241.41000000
9995 1241.41000000
9996 1241.41000000
9997 1241.41000000
9998 1241.41000000
9999 1241.41000000
10073 1660.30000000
10076 1660.30000000
10077 1660.30000000
10079 1660.30000000
10080 1660.30000000
10081 1660.30000000
10082 1660.30000000
10083 1660.30000000
10084 1660.30000000
10085 1660.30000000
10086 1660.30000000
10179 1660.30000000
10180 1660.30000000
10523 1660.30000000
10547 1381.72000000
10584 1660.30000000
10594 1660.30000000
10604 2997.44000000
10605 2997.44000000
10607 1292.58000000
10608 1292.58000000
10609 1292.58000000
10610 1292.58000000
10611 1292.58000000
10612 1292.58000000
10613 1292.58000000
10614 1292.58000000
10615 1292.58000000
10616 1292.58000000
10617 1292.58000000
10618 1292.58000000
10619 1292.58000000
10620 1292.58000000
10621 1292.58000000
10622 1292.58000000
10623 1292.58000000
10624 1292.58000000
10645 1381.72000000
10646 1381.72000000
10647 1381.72000000
10648 1381.72000000
10649 1381.72000000
10650 1381.72000000
10653 1381.72000000
10654 2997.44000000
10655 2997.44000000
10668 1136.58000000
10669 1136.58000000
10670 1136.58000000
10671 1136.58000000
10672 1136.58000000
10673 1136.58000000
10674 1136.58000000
10675 1136.58000000
10676 1136.58000000
10677 1136.58000000
10678 1136.58000000
10679 1136.58000000
10680 1136.58000000
10681 1136.58000000
10682 1136.58000000
10683 1136.58000000
10684 1136.58000000
10685 1136.58000000
10686 1136.58000000
10726 1381.72000000
10734 2294.40000000
10735 2294.40000000
10736 2294.40000000
10737 2294.40000000
10738 2294.40000000
10747 6184.31000000
10748 6184.31000000
10749 6184.31000000
10750 6184.31000000
10751 6184.31000000
10752 6184.31000000
12995 3186.87000000
12996 3186.87000000
12997 3186.87000000
12998 3186.87000000
15732 1136.58000000
15736 3955.73000000
15737 3955.73000000
15738 3955.73000000
15739 3955.73000000
15740 3955.73000000
15741 3955.73000000
15742 3955.73000000
15743 3955.73000000
15744 3000.00000000
15745 3955.73000000
15746 3955.73000000