9R90 | pdb_00009r90

Cryo-EM structure of human ATP citrate lyase in complex with inhibitor EVT0185-CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

ACLY inhibition promotes tumour immunity and suppresses liver cancer.

Gautam, J.Wu, J.Lally, J.S.V.McNicol, J.D.Fayyazi, R.Ahmadi, E.Oniciu, D.C.Heaton, S.Newton, R.S.Rehal, S.Bhattacharya, D.Di Pastena, F.Nguyen, B.Valvano, C.M.Townsend, L.K.Banskota, S.Batchuluun, B.Jabile, M.J.T.Payne, A.Lu, J.Desjardins, E.M.Kubota, N.Tsakiridis, E.E.Mistry, B.Aganostopoulos, A.Houde, V.Dansercoer, A.Verschueren, K.H.G.Savvides, S.N.Hammill, J.A.Bezverbnaya, K.Muti, P.Tsakiridis, T.Dai, W.Jiang, L.Hoshida, Y.Larche, M.Bramson, J.L.Friedman, S.L.Verstraete, K.Wang, D.Steinberg, G.R.

(2025) Nature 645: 507-517

  • DOI: https://doi.org/10.1038/s41586-025-09297-0
  • Primary Citation of Related Structures:  
    9R90

  • PubMed Abstract: 

    Immunosuppressive tumour microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC) (MASH-HCC) 1-3 . Although immune cell metabolism influences effector function, the effect of tumour metabolism on immunogenicity is less understood 4 . ATP citrate lyase (ACLY) links substrate availability and mitochondrial metabolism with lipid biosynthesis and gene regulation 5-7 . Although ACLY inhibition shows antiproliferative effects in various tumours, clinical translation has been limited by challenges in inhibitor development and compensatory metabolic pathways 8-12 . Here, using a mouse model of MASH-HCC that mirrors human disease, genetic inhibition of ACLY in hepatocytes and tumours reduced neoplastic lesions by over 70%. To evaluate the therapeutic potential of this pathway, a novel small-molecule ACLY inhibitor, EVT0185 (6-[4-(5-carboxy-5-methyl-hexyl)-phenyl]-2,2-dimethylhexanoic acid), was identified via phenotypic screening. EVT0185 is converted to a CoA thioester in the liver by SLC27A2 and structural analysis by cryo-electron microscopy reveals that EVT0185-CoA directly interacts with the CoA-binding site of ACLY. Oral delivery of EVT0185 in three mouse models of MASH-HCC dramatically reduces tumour burden as monotherapy and enhances efficacy of current standards of care including tyrosine kinase inhibitors and immunotherapies. Transcriptomic and spatial profiling in mice and humans linked reduced tumour ACLY with increases in the chemokine CXCL13, tumour-infiltrating B cells and tertiary lymphoid structures. The depletion of B cells blocked the antitumour effects of ACLY inhibition. Together, these findings illustrate how targeting tumour metabolism can rewire immune function and suppress cancer progression in MASH-HCC.


  • Organizational Affiliation
    • Centre for Metabolism, Obesity and Diabetes Research, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of ATP-citrate synthase
A, B, C, D
1,120Homo sapiensMutation(s): 0 
Gene Names: ACLY
EC: 2.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for P53396 (Homo sapiens)
Go to UniProtKB:  P53396
PHAROS:  P53396
GTEx:  ENSG00000131473 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53396-2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W1K
Query on W1K

Download Ideal Coordinates CCD File 
F [auth A]6-[4-[6-[2-[3-[[4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-5,5-dimethyl-6-oxidanylidene-hexyl]phenyl]-2,2-dimethyl-hexanoic acid
C43 H68 N7 O19 P3 S
TWFKXKHWAYIPPV-IJQVEXFUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARCv3.1.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium1524918N

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release