This assumes you have reviewed IBM GSKit (Global Security Kit) - Getting Started.

The -delete option can be used to delete a certificate from the key database. You may want to export the certificate before you delete it so that you can import the certificate back into the key database if needed.

${install_root}/gsk8/bin/gsk8capicmd_64
-cert
-delete
-db /path/to/example.kdb
-stashed or -pw your_password
-label "certificate_name"