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 (
    5346, 5387, 5309, 5386, 5370, 5369, 5371, 
    5392, 5390, 5372, 11255, 11277, 10956, 
    11280, 11456, 11118, 11131, 10954, 
    11074, 11222, 11102, 11112, 11069, 
    11099
  ) 
  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 0.00074

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "32.11"
    },
    "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": 58,
        "rows_produced_per_join": 11,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5346,5387,5309,5386,5370,5369,5371,5392,5390,5372,11255,11277,10956,11280,11456,11118,11131,10954,11074,11222,11102,11112,11069,11099))",
        "cost_info": {
          "read_cost": "30.95",
          "eval_cost": "1.16",
          "prefix_cost": "32.11",
          "data_read_per_join": "278"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}