9SXI | pdb_00009sxi

HUMAN CD38 ECTODOMAIN BOUND TO CVN14-ADPR ADDUCT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent, Selective, and Brain-Penetrant Small Molecule CD38 Inhibitors.

Stott, A.J.Burli, R.W.Doyle, K.J.Dickson, L.Hewer, R.C.Pickford, P.Roberts, M.J.Waters-Hall, R.Wu, Y.Zebisch, M.Rangel, V.Geitmann, M.Matthews, K.Brice, N.L.Carlton, M.Dawson, L.A.Harvey, J.R.M.

(2026) ACS Med Chem Lett 17: 259-265

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00727
  • Primary Citation of Related Structures:  
    9SXI

  • PubMed Abstract: 

    Cluster of differentiation 38 (CD38) is a nicotinamide adenine dinucleotide (NAD + )-consuming ectoenzyme abundantly expressed in brain regions involved in motor control and cognition. Given the central role of NAD + in maintaining neuronal health, inhibition of CD38, resulting in NAD + elevation, has emerged as a potential therapeutic approach for neurodegenerative diseases and age-associated cognitive decline. Herein, we report the rational, structure-guided optimization of a series of small-molecule CD38 inhibitors, culminating in the identification of CVN14 , a potent, selective, and brain-penetrant tool molecule with favorable pharmacokinetic properties for advanced preclinical evaluation. We further disclose the first high-resolution X-ray crystal structure of the CVN14- ADPR - CD38 complex, revealing an uncompetitive binding mode. CVN14 provides a molecular tool to investigate CD38 biology in neurodegeneration and supports the development of next-generation brain-penetrant CD38 inhibitors.


  • Organizational Affiliation
    • Cerevance Limited, 418 Cambridge Science Park, Cambridge CB4 0PZ, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1256Homo sapiensMutation(s): 4 
Gene Names: CD38
EC: 3.2.2 (PDB Primary Data), 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens)
Explore P28907 
Go to UniProtKB:  P28907
PHAROS:  P28907
GTEx:  ENSG00000004468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28907
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JSF (Subject of Investigation/LOI)
Query on A1JSF

Download Ideal Coordinates CCD File 
B [auth A][[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[3-[4-methyl-6-[[4-[2,2,2-tris(fluoranyl)ethylamino]cyclohexyl]carbamoyl]pyrimidin-2-yl]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C32 H43 F3 N11 O14 P2
GJVNDADRBKRXQI-CCOYQQLFSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.13α = 90
b = 65.18β = 90
c = 73.36γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Database references