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 (
    6843, 6840, 6841, 6846, 13274, 13286, 
    13280, 13292, 3430, 3429, 3437, 3436, 
    3438, 3477, 3452, 3478, 3479, 3453, 
    3491, 3488, 3497, 3495, 3489, 3492, 
    3496, 3490, 3494, 6951, 3502, 3503, 
    3493, 3498, 3428, 12850, 12869, 12802
  ) 
  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 0.00111

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "46.36"
    },
    "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": 83,
        "rows_produced_per_join": 16,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (6843,6840,6841,6846,13274,13286,13280,13292,3430,3429,3437,3436,3438,3477,3452,3478,3479,3453,3491,3488,3497,3495,3489,3492,3496,3490,3494,6951,3502,3503,3493,3498,3428,12850,12869,12802))",
        "cost_info": {
          "read_cost": "44.70",
          "eval_cost": "1.66",
          "prefix_cost": "46.36",
          "data_read_per_join": "398"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}