4TMF

Crystal structure of human CD38 in complex with hydrolysed compound JMS713


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cyclic adenosine 5'-diphosphate ribose analogs without a "southern" ribose inhibit ADP-ribosyl cyclase-hydrolase CD38.

Swarbrick, J.M.Graeff, R.Zhang, H.Thomas, M.P.Hao, Q.Potter, B.V.

(2014) J.Med.Chem. 57: 8517-8529

  • DOI: 10.1021/jm501037u

  • PubMed Abstract: 
  • Cyclic adenosine 5'-diphosphate ribose (cADPR) analogs based on the cyclic inosine 5'-diphosphate ribose (cIDPR) template were synthesized by recently developed stereo- and regioselective N1-ribosylation. Replacing the base N9-ribose with a butyl cha ...

    Cyclic adenosine 5'-diphosphate ribose (cADPR) analogs based on the cyclic inosine 5'-diphosphate ribose (cIDPR) template were synthesized by recently developed stereo- and regioselective N1-ribosylation. Replacing the base N9-ribose with a butyl chain generates inhibitors of cADPR hydrolysis by the human ADP-ribosyl cyclase CD38 catalytic domain (shCD38), illustrating the nonessential nature of the "southern" ribose for binding. Butyl substitution generally improves potency relative to the parent cIDPRs, and 8-amino-N9-butyl-cIDPR is comparable to the best noncovalent CD38 inhibitors to date (IC50 = 3.3 μM). Crystallographic analysis of the shCD38:8-amino-N9-butyl-cIDPR complex to a 2.05 Å resolution unexpectedly reveals an N1-hydrolyzed ligand in the active site, suggesting that it is the N6-imino form of cADPR that is hydrolyzed by CD38. While HPLC studies confirm ligand cleavage at very high protein concentrations, they indicate that hydrolysis does not occur under physiological concentrations. Taken together, these analogs confirm that the "northern" ribose is critical for CD38 activity and inhibition, provide new insight into the mechanism of cADPR hydrolysis by CD38, and may aid future inhibitor design.


    Organizational Affiliation

    Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath , Claverton Down, Bath, BA2 7AY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
A, B
257Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JS2
Query on JS2

Download SDF File 
Download CCD File 
A, B
5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranose
8-NH2-hypoxanthine-N9-butyl diphosphate ribose
C14 H23 N5 O12 P2
PAHYBMURMGWUSG-HMMKDHSLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.690α = 108.58
b = 54.128β = 90.98
c = 63.319γ = 93.98
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
Blu-Icedata collection
REFMACrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary