Subject: Receptor-ligand complexes

From: [email-masked] (M. Nicklaus)
Date: Thu, 26 Jan 95 14:20:50 -0500

Harry C. Johnson ([email-masked]) wrote:

>I am looking for some simple examples of receptor-ligand structures.
>I would prefer PDB, macromodel, sybyl mol and mol2, or, of course,
>Spartan input files.

For a systematic comparison of the conformations of small molecule
ligands in the crystal (of the pure compound), in a protein binding
site, and in the global energy minimum, we did an extensive survey 
of all receptor-ligand complexes in the PDB.  I am appending the
results of that search to this message.

If you want to search (a newer version of) the PDB, you may want to
search for the string 'HET   ' at the beginning of the line (do add
the blanks in the search strings, otherwise you'll find a lot of
other stuff).  This string denotes lines in the header section of
the PDB files that list "hetero-residues" occurring in the structure.
You'll find a lot of "false positives", such as single atoms or ions;
but in our experience you are less likely to miss valid receptor-
ligand complexes than if you searched the PDB file headers for terms
such as 'COMPLEX', 'LIGAND', 'BOUND' etc.

The following table lists only those ligands for which we found the       
corresponding entry in the Cambridge Structural Database (CSD).
If this condition is not applied, you'll find many more complexes
in the PDB.  In the somewhat older version we searched, we found 
ca. 200 (small molecule) compound names as the set of potentially
interesting ligands.

I hope this may help you.

Compound               PDB File  Protein
------------------------------------------------------------------

ADP                        1pfk  Phosphofructokinase 
                           4pfk  Phosphofructokinase

ATP                        4at1  Aspartate carbamoyltransferase
                           7at1  Aspartate carbamoyltransferase

Biotin                     1stp  Streptavidin

Chloramphenicol            1cla  Chloramphenicol acetyltransferase
                           3cla  Chloramphenicol acetyltransferase
                           4cla  Chloramphenicol acetyltransferase

Citric acid                1cts  Citrate synthase
                           3cts  Citrate synthase
                           5ldh  Lactate dehydrogenase
                           8ldh  Lactate dehydrogenase

Dimethylformamide          6est  Elastase
                           7est  Elastase

Fructose-6-phosphate       1fbp  Fructose-1,6-biphosphatase
                           4pfk  Phosphofructokinase
                           5fbp  Fructose-1,6-biphosphatase

FK506                      1fkf  FK506 binding protein

alpha-D-galactose          8abp  L-Arabinose-binding protein
                           9abp  L-Arabinose-binding protein

beta-D-galactose           8abp  L-Arabinose-binding protein
                           9abp  L-Arabinose-binding protein
beta-D-glucose             3gbp  Galactose-binding protein

p-Hydroxybenzoic acid      2phh  p-Hydroxybenzoate hydroxylase

Isocitric acid             5icd  Isocitrate dehydrogenase

D-Malic acid               4csc  Citrate synthase

L-malic acid               1csc  Citrate synthase
                           3csc  Citrate synthase

Malonic acid               2at1  Aspartate carbamoyltransferase
                           7at1  Aspartate carbamoyltransferase

Maltose                    1mbp  D-Maltodextrin-binding protein

Methotrexate               3dfr  Dihydrofolate reductase
                           4dfr  Dihydrofolate reductase

Oxamic acid                1ldm  Lactate dehydrogenase

2-Phospho-D-glyceric acid  7enl  Enolase

3-Phosphoglyceric acid     3pgk  Phosphoglycerate kinase

PALA                       8atc  Aspartate carbamoyltransferase

Pyridoxamine-5'-phosphate  2aat  Aspartate aminotransferase

Pyruvic acid               3ldh  Lactate dehydrogenase

D-Sorbitol                 4xia  D-Xylose isomerase

Sucrose                    1r1a  Rhinovirus serotype 1 coat protein

Xylitol                    5xia  D-Xylose isomerase

------------------------------------------------------------------------
 Marc C. Nicklaus                        Lab. of Medicinal Chemistry
 e-mail: [email-masked]               National Cancer Institute, NIH
 Phone:  (301) 402-3111                  Bldg 37, Rm 5B29
 Fax:    (301) 496-5839                  BETHESDA, MD 20892-4255
------------------------------------------------------------------------