Hi, there are tow methods for you go to Nanjing from Pudong in terms of your arrival time.
1. take the airport long-distance to Nanjing Zhonghuamen directly. The buses depart from the Shanghai Pudong Airport respectively at 10:20, 12:50, 14:50, 16:50 and 19:20. The ticket fare is 136yuan and the journey takes about 4 or 5 hours.
2. if you miss the airport bus, you'd better go to Nanjing by train from Shanghai Railway Station. The airport shuttle bus Line 5 could drive you to the railway station within one hour. For the train information, it is suggested that you visit:
https://www.travelchinaguide.com/china-trains/