SELECT 
  rate_id, 
  shipping_id, 
  rate_value, 
  destination_id, 
  base_rate 
FROM 
  cscart_shipping_rates 
WHERE 
  shipping_id = 100 
  AND destination_id = 1 
ORDER BY 
  destination_id desc

Query time 0.00014

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "1.00"
    },
    "ordering_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_shipping_rates",
        "access_type": "const",
        "possible_keys": [
          "shipping_rate"
        ],
        "key": "shipping_rate",
        "used_key_parts": [
          "shipping_id",
          "destination_id"
        ],
        "key_length": "6",
        "ref": [
          "const",
          "const"
        ],
        "rows_examined_per_scan": 1,
        "rows_produced_per_join": 1,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "0.00",
          "eval_cost": "0.10",
          "prefix_cost": "0.00",
          "data_read_per_join": "32"
        },
        "used_columns": [
          "rate_id",
          "shipping_id",
          "destination_id",
          "base_rate",
          "rate_value"
        ]
      }
    }
  }
}