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 (
    2603, 3136, 2587, 2761, 2694, 3096, 2723, 
    2742, 3556, 2593, 3104, 2618, 2828, 
    2613, 2619, 2872, 2704, 3593, 4888, 
    3423, 5168, 2739, 3291, 5998, 2841, 
    5155, 3876, 2561, 3812, 5124, 6007, 
    2865, 2734, 3369, 6005, 6019, 3139, 
    5157, 2700, 5121, 5929, 2701, 6013, 
    2797, 6271, 5938, 5980, 4886, 4885, 
    8243, 5933, 6006, 5981, 6024, 5983, 
    8603, 10022, 8272, 7878, 8879, 7880, 
    8458
  ) 
  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 0.00210

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "43.41"
    },
    "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": 62,
        "rows_produced_per_join": 12,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (2603,3136,2587,2761,2694,3096,2723,2742,3556,2593,3104,2618,2828,2613,2619,2872,2704,3593,4888,3423,5168,2739,3291,5998,2841,5155,3876,2561,3812,5124,6007,2865,2734,3369,6005,6019,3139,5157,2700,5121,5929,2701,6013,2797,6271,5938,5980,4886,4885,8243,5933,6006,5981,6024,5983,8603,10022,8272,7878,8879,7880,8458))",
        "cost_info": {
          "read_cost": "42.17",
          "eval_cost": "1.24",
          "prefix_cost": "43.41",
          "data_read_per_join": "297"
        },
        "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)))"
      }
    }
  }
}