3U4I

CD38 structure-based inhibitor design using the N1-cyclic inosine 5'-diphosphate ribose template


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.118 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CD38 Structure-Based Inhibitor Design Using the N1-Cyclic Inosine 5'-Diphosphate Ribose Template

Moreau, C.Liu, Q.Graeff, R.Wagner, G.K.Thomas, M.P.Swarbrick, J.M.Shuto, S.Lee, H.C.Hao, Q.Potter, B.V.L.

(2013) Plos One 8: e66247-e66247

  • DOI: 10.1371/journal.pone.0066247
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Few inhibitors exist for CD38, a multifunctional enzyme catalyzing the formation and metabolism of the Ca(2+)-mobilizing second messenger cyclic adenosine 5'-diphosphoribose (cADPR). Synthetic, non-hydrolyzable ligands can facilitate structure-based ...

    Few inhibitors exist for CD38, a multifunctional enzyme catalyzing the formation and metabolism of the Ca(2+)-mobilizing second messenger cyclic adenosine 5'-diphosphoribose (cADPR). Synthetic, non-hydrolyzable ligands can facilitate structure-based inhibitor design. Molecular docking was used to reproduce the crystallographic binding mode of cyclic inosine 5'-diphosphoribose (N1-cIDPR) with CD38, revealing an exploitable pocket and predicting the potential to introduce an extra hydrogen bond interaction with Asp-155. The purine C-8 position of N1-cIDPR (IC50 276 µM) was extended with an amino or diaminobutane group and the 8-modified compounds were evaluated against CD38-catalyzed cADPR hydrolysis. Crystallography of an 8-amino N1-cIDPR:CD38 complex confirmed the predicted interaction with Asp-155, together with a second H-bond from a realigned Glu-146, rationalizing the improved inhibition (IC50 56 µM). Crystallography of a complex of cyclic ADP-carbocyclic ribose (cADPcR, IC50 129 µM) with CD38 illustrated that Glu-146 hydrogen bonds with the ligand N6-amino group. Both 8-amino N1-cIDPR and cADPcR bind deep in the active site reaching the catalytic residue Glu-226, and mimicking the likely location of cADPR during catalysis. Substantial overlap of the N1-cIDPR "northern" ribose monophosphate and the cADPcR carbocyclic ribose monophosphate regions suggests that this area is crucial for inhibitor design, leading to a new compound series of N1-inosine 5'-monophosphates (N1-IMPs). These small fragments inhibit hydrolysis of cADPR more efficiently than the parent cyclic compounds, with the best in the series demonstrating potent inhibition (IC50 = 7.6 µM). The lower molecular weight and relative simplicity of these compounds compared to cADPR make them attractive as a starting point for further inhibitor design.


    Organizational Affiliation

    Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase 1
A, B
262Homo sapiensMutation(s): 5 
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
CVR
Query on CVR

Download SDF File 
Download CCD File 
A
Cyclic adenosine 5'-diphosphocarbocyclic ribose
C16 H23 N5 O12 P2
WXTUXMLWWNQYJT-BKYLUIDASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CVRIC50: 129000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.118 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.223α = 105.20
b = 53.998β = 91.08
c = 66.547γ = 94.68
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references