OTUB2 in covalent complex with LN5P45

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report

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Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2.

Gan, J.de Vries, J.Akkermans, J.J.L.L.Mohammed, Y.Tjokrodirijo, R.T.N.de Ru, A.H.Kim, R.Q.Vargas, D.A.Pol, V.Fasan, R.van Veelen, P.A.Neefjes, J.van Dam, H.Ovaa, H.Sapmaz, A.Geurink, P.P.

(2023) ACS Chem Biol 18: 2003-2013

  • DOI: https://doi.org/10.1021/acschembio.3c00227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45 , comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.

  • Organizational Affiliation

    Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin thioesterase OTUB2A [auth AAA]236Homo sapiensMutation(s): 0 
Gene Names: OTUB2C14orf137OTB2OTU2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DC9 (Homo sapiens)
Explore Q96DC9 
Go to UniProtKB:  Q96DC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96DC9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2X (Subject of Investigation/LOI)
Query on V2X

Download Ideal Coordinates CCD File 
B [auth AAA](1~{S},2~{S})-~{N}'-ethanoyl-2-(3-methylphenyl)cyclopropane-1-carbohydrazide
C13 H16 N2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.65α = 90
b = 45.25β = 96.05
c = 58γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands724.013.002

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release