SELECT 
  product_prices.product_id, 
  MIN(
    IF(
      product_prices.percentage_discount = 0, 
      product_prices.price, 
      product_prices.price - (
        product_prices.price * product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  product_prices 
WHERE 
  product_prices.product_id IN (
    5978, 2760, 758, 764, 1352, 1390, 2596, 
    2599, 1356, 2595, 1395, 2601, 2600, 
    2598, 1379, 5817, 2768, 5814, 1378, 
    2772, 5843, 5854, 3413, 5956, 5910, 
    3329, 3377, 2543, 5861, 5839, 5830, 
    5801, 5804, 5815, 5849, 5806, 5836, 
    3591, 3374, 5808, 5809, 3409, 6004, 
    5920, 5879, 3403, 5885, 5911
  ) 
  AND product_prices.lower_limit = 1 
  AND product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  product_prices.product_id

Query time 0.00171

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "40.18"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "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": 48,
        "rows_produced_per_join": 4,
        "filtered": "10.00",
        "index_condition": "(`goimagine`.`product_prices`.`product_id` in (5978,2760,758,764,1352,1390,2596,2599,1356,2595,1395,2601,2600,2598,1379,5817,2768,5814,1378,2772,5843,5854,3413,5956,5910,3329,3377,2543,5861,5839,5830,5801,5804,5815,5849,5806,5836,3591,3374,5808,5809,3409,6004,5920,5879,3403,5885,5911))",
        "cost_info": {
          "read_cost": "39.70",
          "eval_cost": "0.48",
          "prefix_cost": "40.18",
          "data_read_per_join": "115"
        },
        "used_columns": [
          "id",
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`goimagine`.`product_prices`.`lower_limit` = 1) and (`goimagine`.`product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}