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 (
    1646, 1647, 1648, 1649, 1650, 1651, 1652, 
    5326, 5327, 5328, 5329, 5330, 5331, 
    5332, 5333, 5334, 5335, 5336, 5337, 
    5338, 5339, 5340, 5341, 5342, 5343, 
    5344, 5345, 5346, 5347, 5348, 5349, 
    5350, 5351, 5352, 2832, 2833, 2834, 
    2835, 6417, 6418, 6419, 6420, 6421, 
    2823, 2824, 2825, 2826, 6408, 6409, 
    6410, 6411, 6412, 2827, 2828, 2829, 
    2830, 2831, 6413, 6414, 6415, 6416, 
    2928, 2929, 2930, 2931, 2932, 6513, 
    6514, 6515, 6516, 3032, 6609, 3028, 
    3029, 3030, 3031, 6605, 6606, 6607, 
    6608, 6610, 6611, 6612, 6613, 3024, 
    3025, 3026, 3027, 3301, 6847, 3300, 
    2841, 2842, 2843, 2844, 6426
  ) 
  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 0.00233

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.21"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 96,
        "rows_produced_per_join": 19,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (1646,1647,1648,1649,1650,1651,1652,5326,5327,5328,5329,5330,5331,5332,5333,5334,5335,5336,5337,5338,5339,5340,5341,5342,5343,5344,5345,5346,5347,5348,5349,5350,5351,5352,2832,2833,2834,2835,6417,6418,6419,6420,6421,2823,2824,2825,2826,6408,6409,6410,6411,6412,2827,2828,2829,2830,2831,6413,6414,6415,6416,2928,2929,2930,2931,2932,6513,6514,6515,6516,3032,6609,3028,3029,3030,3031,6605,6606,6607,6608,6610,6611,6612,6613,3024,3025,3026,3027,3301,6847,3300,2841,2842,2843,2844,6426))",
        "cost_info": {
          "read_cost": "65.29",
          "eval_cost": "1.92",
          "prefix_cost": "67.21",
          "data_read_per_join": "460"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}