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 (
    431561, 431562, 431563, 431564, 431565, 
    431566, 431567, 431568, 431569, 431587, 
    431588, 431589, 431590, 431591, 431592, 
    431593, 431594, 431595, 431596, 431597, 
    431598, 431599, 431600, 431601, 431602, 
    431603, 431604
  ) 
  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 0.00244

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "75.69"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 54,
        "rows_produced_per_join": 54,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "64.89",
          "eval_cost": "10.80",
          "prefix_cost": "75.69",
          "data_read_per_join": "3K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (431561,431562,431563,431564,431565,431566,431567,431568,431569,431587,431588,431589,431590,431591,431592,431593,431594,431595,431596,431597,431598,431599,431600,431601,431602,431603,431604)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}