SELECT 
  product_id, 
  amount 
FROM 
  cscart_warehouses_destination_products_amount 
WHERE 
  product_id IN (3963) 
  AND destination_id = 12 
  AND storefront_id = 0

Query time 0.00091

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "1.00"
    },
    "table": {
      "table_name": "cscart_warehouses_destination_products_amount",
      "access_type": "const",
      "possible_keys": [
        "PRIMARY",
        "idx_storefront_id"
      ],
      "key": "PRIMARY",
      "used_key_parts": [
        "product_id",
        "destination_id",
        "storefront_id"
      ],
      "key_length": "9",
      "ref": [
        "const",
        "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": "16"
      },
      "used_columns": [
        "destination_id",
        "storefront_id",
        "product_id",
        "amount"
      ]
    }
  }
}