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 (
    6560, 6613, 6612, 6616, 6615, 6611, 54762, 
    54754, 54778, 54773, 54772, 54748, 
    54759, 54753, 54747, 54741, 54751, 
    54761, 54776, 54757, 54770, 54745, 
    54750, 54764, 54766, 54774, 54775, 
    54743
  ) 
  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 0.00102

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "19.61"
    },
    "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": 28,
        "rows_produced_per_join": 5,
        "filtered": "20.00",
        "index_condition": "(`cscartdb`.`cscart_product_prices`.`product_id` in (6560,6613,6612,6616,6615,6611,54762,54754,54778,54773,54772,54748,54759,54753,54747,54741,54751,54761,54776,54757,54770,54745,54750,54764,54766,54774,54775,54743))",
        "cost_info": {
          "read_cost": "19.05",
          "eval_cost": "0.56",
          "prefix_cost": "19.61",
          "data_read_per_join": "134"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`cscartdb`.`cscart_product_prices`.`lower_limit` = 1) and (`cscartdb`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}