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 (
    10708, 10709, 10710, 10711, 10712, 10301, 
    10302, 10303, 10304, 9945, 10601, 9727, 
    9728, 9729, 9730, 9731, 9732, 9733, 
    10181, 9734, 9735, 9724, 10370, 10372, 
    10374, 10376, 10377, 10378, 10379, 
    10380, 10381, 10371, 10373, 10375, 
    10387, 10395, 10390, 10394, 10393, 
    10392, 10386, 10389, 10388, 10637, 
    10638, 10639, 10640, 10641, 13013, 
    13014, 13015, 13016, 13017, 13018, 
    13019, 13020, 13021, 13022, 13023, 
    13024, 13025, 13026, 13027, 13028
  ) 
  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 0.00097

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 (10708,10709,10710,10711,10712,10301,10302,10303,10304,9945,10601,9727,9728,9729,9730,9731,9732,9733,10181,9734,9735,9724,10370,10372,10374,10376,10377,10378,10379,10380,10381,10371,10373,10375,10387,10395,10390,10394,10393,10392,10386,10389,10388,10637,10638,10639,10640,10641,13013,13014,13015,13016,13017,13018,13019,13020,13021,13022,13023,13024,13025,13026,13027,13028)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9724 1482.01000000
9727 1482.01000000
9728 1482.01000000
9729 1482.01000000
9730 1482.01000000
9731 1482.01000000
9732 1482.01000000
9733 1482.01000000
9734 1482.01000000
9735 1482.01000000
9945 1482.01000000
10181 1482.01000000
10301 4579.74000000
10302 4579.74000000
10303 4579.74000000
10304 4579.74000000
10370 2763.44000000
10371 2763.44000000
10372 2763.44000000
10373 2763.44000000
10374 2763.44000000
10375 2763.44000000
10376 2763.44000000
10377 2763.44000000
10378 2763.44000000
10379 2763.44000000
10380 2763.44000000
10381 2763.44000000
10386 2540.59000000
10387 2540.59000000
10388 2540.59000000
10389 2540.59000000
10390 2540.59000000
10392 2540.59000000
10393 2540.59000000
10394 2540.59000000
10395 2540.59000000
10601 1482.01000000
10637 2540.59000000
10638 2540.59000000
10639 2540.59000000
10640 2540.59000000
10641 2540.59000000
10708 3432.02000000
10709 3432.02000000
10710 3432.02000000
10711 3432.02000000
10712 3432.02000000
13013 1927.73000000
13014 1927.73000000
13015 1927.73000000
13016 1927.73000000
13017 1927.73000000
13018 1927.73000000
13019 1927.73000000
13020 1927.73000000
13021 1927.73000000
13022 1927.73000000
13023 1927.73000000
13024 1927.73000000
13025 1927.73000000
13026 1927.73000000
13027 1927.73000000
13028 1927.73000000