3ROK image
Deposition Date 2011-04-26
Release Date 2011-12-21
Last Version Date 2024-10-16
Entry Detail
PDB ID:
3ROK
Title:
Crystal structure of human CD38 in complex with compound CZ-27
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.65 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ADP-ribosyl cyclase 1
Gene (Uniprot):CD38
Mutations:N100D, N164D, N219D, N209D
Chain IDs:A, B
Chain Length:254
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Catalysis-based inhibitors of the calcium signaling function of CD38.
Biochemistry 51 555 564 (2012)
PMID: 22142305 DOI: 10.1021/bi201509f

Abstact

CD38 is a signaling enzyme responsible for catalyzing the synthesis of cyclic ADP ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate; both are universal Ca(2+) messenger molecules. Ablation of the CD38 gene in mice causes multiple physiological defects, including impaired oxytocin release, that result in altered social behavior. A series of catalysis-based inhibitors of CD38 were designed and synthesized, starting with arabinosyl-2'-fluoro-2'-deoxynicotinamide mononucleotide. Structure-function relationships were analyzed to assess the structural determinants important for inhibiting the NADase activity of CD38. X-ray crystallography was used to reveal the covalent intermediates that were formed with the catalytic residue, Glu226. Metabolically stable analogues that were resistant to inactivation by phosphatase and esterase were synthesized and shown to be effective in inhibiting intracellular cADPR production in human HL-60 cells during induction of differentiation by retinoic acid. The inhibition was species-independent, and the analogues were similarly effective in blocking the cyclization reaction of CD38 in rat ventricular tissue extracts, as well as inhibiting the α-agonist-induced constriction in rat mesentery arteries. These compounds thus represent the first generally applicable and catalysis-based inhibitors of the Ca(2+) signaling function of CD38.

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Primary Citation of related structures