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 (
    11964, 18422, 11851, 11814, 11672, 11852, 
    12946, 11919, 11853, 11673, 13219, 
    13349, 11815, 11674, 12421, 13087, 
    11675, 7778, 6943, 11854, 13382, 13168, 
    11731, 13383, 12516, 12517, 7278, 11941, 
    11942, 11676, 8062, 11677, 11678, 11732, 
    12947, 7995, 11733, 12214, 13073, 13384, 
    13385, 11734, 11943, 13350, 12518, 
    7896, 11855, 11679, 11856, 13386, 7541, 
    11850, 11680, 13074, 11681, 12215, 
    9699, 11857, 12948, 12949, 11682, 11683, 
    11805, 11684, 11735, 11858, 12216, 
    11685, 11736, 11686, 11687, 11688, 
    8159, 11859, 11737, 11689, 12950, 11944, 
    11860, 12217, 11738, 13262, 13387, 
    11816, 11861, 7658, 8377, 11862, 11863, 
    13089, 11690, 12073, 11864, 11739, 
    13169, 7161, 18099, 11865, 12519, 12520
  ) 
  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 0.01677

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 11706,
              "filtered": 100,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (11964,18422,11851,11814,11672,11852,12946,11919,11853,11673,13219,13349,11815,11674,12421,13087,11675,7778,6943,11854,13382,13168,11731,13383,12516,12517,7278,11941,11942,11676,8062,11677,11678,11732,12947,7995,11733,12214,13073,13384,13385,11734,11943,13350,12518,7896,11855,11679,11856,13386,7541,11850,11680,13074,11681,12215,9699,11857,12948,12949,11682,11683,11805,11684,11735,11858,12216,11685,11736,11686,11687,11688,8159,11859,11737,11689,12950,11944,11860,12217,11738,13262,13387,11816,11861,7658,8377,11862,11863,13089,11690,12073,11864,11739,13169,7161,18099,11865,12519,12520) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}