[phenixbb] covalently linked ligand

Charles Stewart Jr., PhD cstewart at salk.edu
Fri Jun 8 09:40:16 PDT 2012

Hello all,

I saw a couple of posts on this from a year ago but didn't find a
conclusive answer to how to tell phenix to insert a covalent bond between
a cysteine residue  and a bound inhibitor. I have the inhibitor (a small
molecule) modeled in but haven't figured out how to insert the covalent
bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a
cif file. The distance between the sulfur on the cysteine and the first
carbon atom in the inhibitor is 1.8A.

Do I need to run eLBOW using the protein-inhibitor pdb to generate an
appropriate cif file?

I see in phenix.refine under the PDB interpretation tab their is a box for
"add link to CIF"....is this where I need to tell phenix to insert the
covalent bond?

I guess I could just draw the inhibitor-cysteine complex as a modified
amino acid and try inserting it that way.....

Charles Stewart Jr., PhD
Research Associate
Chemical Biology and Proteomics Laboratory-Noel
Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA 92037

Phone: (858) 453-4100 x1946
Fax: (858) 597-0855
Email: cstewart at salk.edu

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