Hi Siddhesh,
Please check the Implementation guide of SAPSSO Secure login: http://help.sap.com/download/sapsso/secure_login_impl_guide_en.pdf
chapter 2.6.5 Using Secure Login Client Profiles for Kerberos and Microsoft Cryptography API Tokens for the configuration to select either the kerberos or the certificate from MS Store for SNC login to an ABAP System.
KR
Valerie