8VAU

Nicotinamide Riboside and CD38: Covalent Inhibition and Live-Cell Labeling

• PDB DOI: https://doi.org/10.2210/pdb8VAU/pdb

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


• Deposited: 2023-12-11 Released: 2024-11-06 
• Deposition Author(s): Kao, G., Zhang, X.N., Nasertorabi, F., Katz, B.B., Li, Z., Dai, Z., Zhang, Z., Zhang, L., Louie, S.G., Cherezov, V., Zhang, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB), National Institutes of Health/National Cancer Institute (NIH/NCI), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Nicotinamide Riboside and CD38: Covalent Inhibition and Live-Cell Labeling

Kao, G., Zhang, X.N., Nasertorabi, F., Katz, B.B., Li, Z., Dai, Z., Zhang, Z., Zhang, L., Louie, S.G., Cherezov, V., Zhang, Y.

(2024) JACS Au 

• DOI: https://doi.org/10.1021/jacsau.4c00695

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.34 kDa 
• Atom Count: 4,457 
• Modelled Residue Count: 499 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NNR (Subject of Investigation/LOI)	C [auth A], E [auth B]	Nicotinamide riboside C11 H15 N2 O5 JLEBZPBDRKPWTD-TURQNECASA-O
RIB (Subject of Investigation/LOI)	D [auth A], F [auth B]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.627	α = 90
b = 51.351	β = 97.26
c = 100.501	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Kao, G., Zhang, X.N., Nasertorabi, F., Katz, B.B., Li, Z., Dai, Z., Zhang, Z., Zhang, L., Louie, S.G., Cherezov, V., Zhang, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM137901
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	R01EB031830
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA276240
Other private		--

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release