6EDR | pdb_00006edr

Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+

• PDB DOI: https://doi.org/10.2210/pdb6EDR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2018-08-10 Released: 2018-11-21 
• Deposition Author(s): Dai, Z., Zhang, X.N., Nasertorabi, F., Cheng, Q., Pei, H., Louie, S.G., Stevens, C.R., Zhang, Y.
• Funding Organization(s): Other private, National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Facile chemoenzymatic synthesis of a novel stable mimic of NAD.

Dai, Z., Zhang, X.N., Nasertorabi, F., Cheng, Q., Pei, H., Louie, S.G., Stevens, R.C., Zhang, Y.

(2018) Chem Sci 9: 8337-8342

• PubMed: 30568770 
• DOI: https://doi.org/10.1039/c8sc03899f
• Primary Citation Related Structures: 
  6EDR


• PubMed Abstract: 
  

  Nicotinamide adenine dinucleotide (NAD ⁺ ) is an essential cofactor participating in a variety of important enzyme-catalyzed physiological and pathophysiological processes. Analogues of NAD ⁺ provide key and valuable agents for investigating NAD ⁺ -dependent enzymes. In this study, we report the preparation of a novel stable NAD ⁺ mimic, 4'-thioribose NAD ⁺ (S-NAD ⁺ ), using a facile and efficient chemoenzymatic approach. Substrate activity assays indicated the resulting S-NAD ⁺ is chemically inert to human CD38 and sirtuin 2 enzymes, but capable of participating in redox reactions in a manner similar to NAD ⁺ . X-ray crystallographic analysis revealed binding of S-NAD ⁺ to the active site of human CD38 and critical residues involved in leaving group activation and catalysis. By more closely mimicking NAD ⁺ in geometry and electrostatics, the generated S-NAD ⁺ offers a unique and important tool that can be extended to study enzymes utilizing NAD ⁺ .

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Organizational Affiliation: 
• Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA . Email: [e-mail].
Departments of Biological Sciences and Chemistry , Bridge Institute , Michelson Center for Convergent Bioscience , University of Southern California , Los Angeles , CA 90089 , USA . Email: [e-mail].
Titus Family Department of Clinical Pharmacy , School of Pharmacy , University of Southern California , 1985 Zonal Ave , Los Angeles , CA 90089 , USA.
Department of Chemistry , Dornsife College of Letters, Arts and Sciences , University of Southern California , Los Angeles , CA 90089 , USA.
Norris Comprehensive Cancer Center , University of Southern California , Los Angeles , CA 90089 , USA.
Research Center for Liver Diseases , University of Southern California , Los Angeles , CA 90089 , USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.89 kDa 
• Atom Count: 4,083 
• Modeled Residue Count: 495 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	A, B	257	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZNA (Subject of Investigation/LOI)	C [auth A], D [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C21 H28 N7 O13 P2 S YLEHCOOOOOOSDX-NNYOXOHSSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.742	α = 90
b = 51.106	β = 96.89
c = 100.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Dai, Z., Zhang, X.N., Nasertorabi, F., Cheng, Q., Pei, H., Louie, S.G., Stevens, C.R., Zhang, Y.

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Funding Organization	Location	Grant Number
Other private	United States	V2016-021
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30DK048522

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-05-15
  Changes: Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Structure summary