9HZ5 | pdb_00009hz5

Pre-clinical characterization of novel multi-client inhibitors of Sec61 with broad anti-tumor activity


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Preclinical characterization of novel multi-client inhibitors of Sec61 with broad antitumor activity.

Lowe, E.Anderl, J.L.Bade, D.Delgado-Martin, C.Dong, C.Fan, R.A.Fang, Y.Jiang, J.Johnson, H.W.B.Kempema, A.McGilvray, P.McMinn, D.Millare, B.Muchamuel, T.Poweleit, N.Qian, Y.Rehan, S.Scapin, G.Sugahara, A.Tranter, D.Tuch, B.Wang, J.Wang, L.Whang, J.A.Zuno-Mitchell, P.Paavilainen, V.O.Park, E.Taunton, J.Kirk, C.J.Anand, N.K.

(2025) J Pharmacol Exp Ther 392: 103634-103634

  • DOI: https://doi.org/10.1016/j.jpet.2025.103634
  • Primary Citation of Related Structures:  
    9D6L, 9HZ5

  • PubMed Abstract: 

    The Sec61 translocon mediates entry of most secreted and transmembrane proteins into the endoplasmic reticulum, providing a novel therapeutic target to block the expression of protumorigenic factors. Sec61 inhibitors with antitumor activity, mostly derived from natural products, have been reported. However, poor tolerability and suboptimal pharmaceutical properties have precluded their further development. We report here the discovery and characterization of KZR-834 and KZR-261, related small molecule analogs that directly bind to the Sec61 channel to potently inhibit the biogenesis of a subset of Sec61 client proteins. This client inhibition profile includes several tumorigenic factors, results in the activation of an endoplasmic reticulum stress response, and leads to broad anticancer effects in vitro. In vivo, KZR-261 was well tolerated and exhibits antitumor effects across multiple models, both as a single agent and in combination with anti-PD-1 immunotherapy. Based on the strength of this preclinical data, KZR-261 progressed into a phase I clinical trial (NCT05047536) in patients with malignant disease, where it was found to be well tolerated at doses that achieved durable stable disease. These results highlight the potential of Sec61 inhibition as a novel therapeutic target. SIGNIFICANCE STATEMENT: KZR-834 and KZR-261 are novel Sec61 inhibitors with the ability to block multiple Sec61 client proteins, leading to well-tolerated efficacy in in vivo cancer models. This represents a novel mechanism for blocking expression of oncogenic factors, including those not amenable to targeting through conventional methods.


  • Organizational Affiliation
    • Kezar Life Sciences, South San Francisco, California.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alphaA [auth B]412Ovis ariesMutation(s): 0 
UniProt
Find proteins for F7G1S7 (Ornithorhynchus anatinus)
Explore F7G1S7 
Go to UniProtKB:  F7G1S7
Entity Groups  
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UniProt GroupF7G1S7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaB [auth A]59Ovis ariesMutation(s): 0 
UniProt
Find proteins for A0A6I8MX59 (Ornithorhynchus anatinus)
Explore A0A6I8MX59 
Go to UniProtKB:  A0A6I8MX59
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UniProt GroupA0A6I8MX59
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit beta20Ovis ariesMutation(s): 0 
UniProt
Find proteins for R0L5M3 (Anas platyrhynchos)
Explore R0L5M3 
Go to UniProtKB:  R0L5M3
Entity Groups  
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UniProt GroupR0L5M3
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A2B
Query on A1A2B

Download Ideal Coordinates CCD File 
D [auth B]4-{(3S)-9-(cyclohexylmethyl)-5-[(3R,5R)-4-(3-fluoro-5-methoxyphenyl)-3,5-dimethylpiperazine-1-sulfonyl]-3-methyl-1,5,9-triazacyclododecane-1-sulfonyl}-N,N-dimethylaniline
C38 H61 F N6 O5 S2
LIDUHPAGWLBVCL-DCMFLLSESA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland338836
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Database references