3ROP

Crystal structure of human CD38 in complex with compound CZ-50b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalysis-based inhibitors of the calcium signaling function of CD38.

Kwong, A.K.Chen, Z.Zhang, H.Leung, F.P.Lam, C.M.Ting, K.Y.Zhang, L.Hao, Q.Zhang, L.H.Lee, H.C.

(2012) Biochemistry 51: 555-564

  • DOI: 10.1021/bi201509f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 physi ...

    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.


    Organizational Affiliation

    Department of Physiology, 4/F Lab Block, University of Hong Kong, Hong Kong.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase 1
A, B
254Homo sapiensMutation(s): 4 
Gene Names: CD38
EC: 3.2.2.6
Find proteins for P28907 (Homo sapiens)
Go to Gene View: CD38
Go to UniProtKB:  P28907
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCA
Query on NCA

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N
 Ligand Interaction
50A
Query on 50A

Download SDF File 
Download CCD File 
A, B
2-deoxy-2-fluoro-5-O-phosphono-alpha-D-ribofuranose
Inhibitor CZ-50b based on arabinosyl-2-fluoro-2-deoxynicotinamide mononucleotide, bound form
C5 H10 F O7 P
NOTDWSJIOCLYHZ-AIHAYLRMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.817α = 109.72
b = 53.630β = 91.19
c = 63.540γ = 94.81
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKLdata processing
HKLdata reduction
REFMACrefinement
HKLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references, Non-polymer description