Primary Citation PubMed: 23840430
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
CD38 Structure-Based Inhibitor Design Using the N1-Cyclic Inosine 5'-Diphosphate Ribose Template.
(2013) PLoS One 8
PubMed: 23840430 | PubMedCentral: PMC3686795 | DOI: 10.1371/journal.pone.0066247
In contrast, docking the 8-NH 2 - N 1-IMP ligand into the 3U4H crystal structure gave two contrasting top-ranked results ( Figures 13B and C ).
N 1-IMP Analogues The 2PGJ and 3U4H crystal structures of human CD38 with cIDPR and 8-amino cIDPR, respectively, were passed through the Protein Preparation Wizard of the Schrödinger software running under Maestro version 9.3.026: the incorrect planar ribose in the 2PGJ structure was manually corrected so that the ribose had the appropriate structure and stereochemistry.
g013 Figure 13 The 3U4H crystal structure with docked ligands.
The ligand in the prepared 2PGJ and 3U4H crystal structures was modified so that the “southern” ribose phosphate was deleted.
To further investigate the binding of the N 1-IMP fragments, we docked the four ligands into two crystal structures of CD38; the 2PGJ structure with N 1-cIDPR as ligand, and the 3U4H structure reported here with 8-NH 2 -cIDPR as the ligand.
Structural Data The atomic coordinates and structure factors of CD38/8-amino N 1-cIDPR and CD38/cADPcR have been deposited with the Protein Data Bank ( www.pdb.org ) with the accession codes 3U4H and 3U4I, respectively.
However, when the four ligands were docked into the 3U4H structure, strikingly different poses were adopted by the ligands depending on their 8-substituents.
Publication Year: 2013
Cyclic adenosine 5'-diphosphate ribose analogs without a "southern" ribose inhibit ADP-ribosyl cyclase-hydrolase CD38.
(2014) J Med Chem 57
PubMed: 25226087 | PubMedCentral: PMC4207131 | DOI: 10.1021/jm501037u
39 − 41 Crystal structures obtained with shCD38 and unnatural ligands 2 (PDB code 2PGJ), 42 cyclic adenosine 5′-diphosphate carbocyclic ribose (cADPcR, 3UHI), 43 and 8-NH 2 -cIDPR (3U4... ) suggest a critical role for the base and “northern” ribose in the binding of cADPR analogs to CD38, as might be predicted for the locus of both cADPR formation and degradation.
Examination of the crystal structures 2PGJ and 3U4H suggests that both binding sites contain two water molecules close to the N 1-link of the cyclic ligand.
Scheme 4 Proposed Mechanism for Hydrolysis of 7 by a High Concentration of shCD38 Figure 6 Docking of 8-NH 2 - N 9-butyl-cIDPR ( 7 ) into 3U4H after removal of ligand (ligand carbons in pink sticks, protein carbons in green).
Publication Year: 2014
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.