10LP | pdb_000010lp

Crystal structure of mouse CD38 with compound 9

• PDB DOI: https://doi.org/10.2210/pdb10LP/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2026-01-27 Released: 2026-10-07 
• Deposition Author(s): Brosey, C.A., Bigelow, L., Chapman, A., Afanador, G., Hodges, T.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.228 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Design and Exploration of a Tricyclic Series of CNS-Penetrant CD38 Small Molecule Inhibitors.

Hodges, T.R., Jang, Y., Korch, K., Osuma, A., Randolph, J.T., Shiroodi, R., Bergstrom, B.D., Brosey, C., Jejurkar, P., Sheehan, M.M., Sadowski, R.N., Lin, K.A., Brown, J.W., Balakrishnan, A., Zoi, I., Bigelow, L., Jain, R., Bradley, N.P., Chapman, A., Korepanova, A., Swensen, A.M., Benekareddy, M., Shotwell, J.B.

(2026) ACS Med Chem Lett 17: 2160-2167

• PubMed: 42866454 
• DOI: https://doi.org/10.1021/acsmedchemlett.6c00301
• Primary Citation Related Structures: 
  10LP, 10OT


• PubMed Abstract: 
  

  Cluster of Differentiation 38 (CD38) plays a key role in NAD ⁺ metabolism and calcium signaling, and recent reports highlight therapeutic opportunities for CD38 modulation in central nervous system (CNS) disorders. In this report, we describe the rational design, synthesis, and exploration of structure-activity relationships (SAR) for a novel and brain-penetrant series of tricyclic compounds that form an adduct with ADPR to inhibit CD38 in an uncompetitive manner. Rigidification of the bioactive conformation via covalent tethering of a 6-membered heteroaromatic core to an imidazole warhead served as the key design element that afforded improved biochemical potency against both mouse and human CD38. Incremental property-based optimization of core and linker motifs generated analogues with enhanced unbound brain-to-plasma ratios in mice. These efforts led to the discovery of brain-penetrant CD38 inhibitor 16 , which was evaluated in vivo and demonstrated dose-dependent increases of NAD ⁺ measured in mouse brain and lung tissue samples following oral doses ranging from 3 to 100 mg/kg.

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Organizational Affiliation: 
• AbbVie, Inc., North Chicago, Illinois 60064, United States.
AbbVie, Inc., South San Francisco, California 94080, United States.
Calico Life Sciences LLC, South San Francisco, California 94080, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.1 kDa 
• Atom Count: 2,230 
• Modeled Residue Count: 243 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	A	263	Mus musculus	Mutation(s): 5  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 P56528 (Mus musculus) Explore P56528  Go to UniProtKB:  P56528
IMPC:  MGI:107474

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1C6U	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-[13-(1-cyclopropylsulfonylpyrazol-4-yl)-9-oxa-4$l^{4},6,12,14-tetrazatricyclo[8.4.0.0^{2,6}]tetradeca-1(14),2,4,10,12-pentaen-4-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C30 H36 N11 O16 P2 S YSMTXHPBMCVYSO-ZTVSOPISSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.228 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.585	α = 90
b = 57.26	β = 90
c = 58.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Brosey, C.A., Bigelow, L., Chapman, A., Afanador, G., Hodges, T.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release
  
• Version 1.1: 2026-10-28
  Changes: Database references