8D0M | pdb_00008d0m

Human CD38 ectodomain bound to a 78c-ADPR adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease.

Bratkowski, M.Burdett, T.C.Danao, J.Wang, X.Mathur, P.Gu, W.Beckstead, J.A.Talreja, S.Yang, Y.S.Danko, G.Park, J.H.Walton, M.Brown, S.P.Tegley, C.M.Joseph, P.R.B.Reynolds, C.H.Sambashivan, S.

(2022) Neuron 110: 3711

  • DOI: https://doi.org/10.1016/j.neuron.2022.08.017
  • Primary Citation Related Structures: 
    8D0C, 8D0D, 8D0E, 8D0F, 8D0G, 8D0H, 8D0I, 8D0J, 8D0M

  • PubMed Abstract: 

    Axon degeneration is an early pathological event in many neurological diseases. The identification of the nicotinamide adenine dinucleotide (NAD) hydrolase SARM1 as a central metabolic sensor and axon executioner presents an exciting opportunity to develop novel neuroprotective therapies that can prevent or halt the degenerative process, yet limited progress has been made on advancing efficacious inhibitors. We describe a class of NAD-dependent active-site SARM1 inhibitors that function by intercepting NAD hydrolysis and undergoing covalent conjugation with the reaction product adenosine diphosphate ribose (ADPR). The resulting small-molecule ADPR adducts are highly potent and confer compelling neuroprotection in preclinical models of neurological injury and disease, validating this mode of inhibition as a viable therapeutic strategy. Additionally, we show that the most potent inhibitor of CD38, a related NAD hydrolase, also functions by the same mechanism, further underscoring the broader applicability of this mechanism in developing therapies against this class of enzymes.


  • Organizational Affiliation
    • Biology Department, Nura Bio Inc., South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 31.63 kDa 
  • Atom Count: 2,101 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 265 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1265Homo sapiensMutation(s): 4 
Gene Names: CD38
EC: 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data), 3.2.2 (UniProt)
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q2C
(Subject of Investigation/LOI)

Query on Q2C



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-[5-[4-[[4-(2-methoxyethoxy)cyclohexyl]amino]-1-methyl-2-oxidanylidene-quinolin-6-yl]-1,3-thiazol-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C37 H49 N8 O16 P2 S
VISHSDFFEFTKEI-QBEAZOKTSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.612α = 90
b = 129.018β = 90
c = 81.712γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary