9IWT | pdb_00009iwt

Crystal structure of human NAMPT complexed with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.187 (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 1.1 of the entry. See complete history

Literature

The NAMPT enzyme employs a switch that directly senses AMP/ATP and regulates cellular responses to energy stress.

Zu, Y.Wu, C.Li, F.Yao, H.Xia, Y.Zhang, R.Li, L.Chen, S.Shi, Q.Xi, S.Pang, H.Liu, M.Wang, L.Terpack, S.Wang, W.Chen, S.Zhang, H.Wang, Y.Yang, M.Huang, S.Zhou, F.Tang, Y.Hu, Z.Fan, S.Tang, Y.Lee, Y.S.Wang, G.

(2025) Mol Cell 85: 2271-2286.e6

  • DOI: https://doi.org/10.1016/j.molcel.2025.05.022
  • Primary Citation Related Structures: 
    9IWT

  • PubMed Abstract: 

    Nicotinamide adenine dinucleotide (NAD + ) is a crucial compound in energy metabolism and cell signaling. Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme responsible for NAD + biosynthesis from nicotinamide (NAM). Here, we report that NAMPT activity is inhibited by adenosine monophosphate (AMP) in response to energy stress. Our global metabolite-protein interaction mapping reveals that NAMPT differentially interacts with AMP from fasted mouse livers. Crystal structures of NAMPT-AMP show that AMP binds similarly to the NAMPT reaction product, nicotinamide mononucleotide (NMN). The inhibition of NAMPT by AMP can be relieved by NAMPT activators or adenosine triphosphate (ATP), likely in a competitive manner. Based on these findings, we further investigated upstream factors contributing to AMP accumulation and found that activation of purine synthesis unexpectedly promotes the rise of AMP during fasting. Notably, an increased AMP/ATP ratio correlates with NAD + decline in ischemic stroke models, in which NAMPT activators can otherwise confer protection.


  • Organizational Affiliation
    • Institute for Translational Medicine on Cell Fate and Disease, Shanghai Ninth People's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Pharmaceutical Sciences, Beijing Frontier Research Center for Biological Structure, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 227.92 kDa 
  • Atom Count: 16,029 
  • Modeled Residue Count: 1,843 
  • Deposited Residue Count: 1,988 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B, C, D
497Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
GTEx:  ENSG00000105835 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
(Subject of Investigation/LOI)

Query on AMP



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
L [auth C],
P [auth D]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
J [auth B]
K [auth B]
M [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
O [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.17α = 90
b = 93.374β = 90
c = 241.942γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81872874
National Natural Science Foundation of China (NSFC)China91949101

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Database references