9ATV | pdb_00009atv

X-ray co-crystal structure of NCGC00685960 / NCATS-SM9335 in NNMT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.201 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

NNMT inhibition in cancer-associated fibroblasts restores antitumour immunity.

Heide, J.Bilecz, A.J.Patnaik, S.Allega, M.F.Donle, L.Yang, K.Teich, E.Li, Y.Lin, Q.Kong, K.Liu, L.Yang, T.G.Cheng, K.C.Shrimp, J.H.Hanson, Q.M.Shen, M.Sun, H.Shah, H.Schweizer, L.Zawieracz, K.Olland, A.White, A.Suto, R.K.Alhunayan, R.Tasdemir, M.Longman, N.Liang, H.Mann, M.Stott, G.M.Hall, M.D.Schworer, S.Weichselbaum, R.R.Piffko, A.Lengyel, E.

(2025) Nature 645: 1051-1059

  • DOI: https://doi.org/10.1038/s41586-025-09303-5
  • Primary Citation of Related Structures:  
    9ATV

  • PubMed Abstract: 

    Cancer-associated fibroblasts (CAFs) have a pivotal cancer-supportive role, yet CAF-targeted therapies are lacking 1,2 . Here, using spatial transcriptomics and single-cell RNA sequencing, we investigate the role of nicotinamide N-methyltransferase (NNMT) in high-grade serous ovarian cancer. Mechanistically, NNMT-induced H3K27me3 hypomethylation drives complement secretion from CAFs, attracting immunosuppressive myeloid-derived suppressor cells (MDSCs) to the tumour. Nnmt knockout in immunocompetent mice impairs tumour growth in syngeneic ovarian, breast and colon tumour models through enhanced CD8 + T cell activation. Using high-throughput screening, we develop a potent and specific NNMT inhibitor that reduces the tumour burden and metastasis in multiple mouse cancer models and restores immune checkpoint blockade efficacy by decreasing CAF-mediated recruitment of MDSCs and reinvigorating CD8 + T cell activation. Our findings establish NNMT as a central CAF regulator and a promising therapeutic target to mitigate immunosuppression in the tumour microenvironment.


  • Organizational Affiliation
    • Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferase
A, B, C
283Homo sapiensMutation(s): 3 
Gene Names: NNMT
EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens)
Explore P40261 
Go to UniProtKB:  P40261
PHAROS:  P40261
GTEx:  ENSG00000166741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40261
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.201 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.596α = 90
b = 91.596β = 90
c = 213.257γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references
  • Version 1.2: 2025-10-08
    Changes: Database references