7KXI

Structure of XL5-ligated hRpn13 Pru domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma.

Lu, X.Sabbasani, V.R.Osei-Amponsa, V.Evans, C.N.King, J.C.Tarasov, S.G.Dyba, M.Das, S.Chan, K.C.Schwieters, C.D.Choudhari, S.Fromont, C.Zhao, Y.Tran, B.Chen, X.Matsuo, H.Andresson, T.Chari, R.Swenson, R.E.Tarasova, N.I.Walters, K.J.

(2021) Nat Commun 12: 7318-7318

  • DOI: 10.1038/s41467-021-27570-4
  • Primary Citation of Related Structures:  
    7KXI

  • PubMed Abstract: 
  • Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition ...

    Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru β-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13 Pru ) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13 Pru , causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13 Pru -producing cancer types.


    Organizational Affiliation

    Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. kylie.walters@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasomal ubiquitin receptor ADRM1A154Homo sapiensMutation(s): 0 
Gene Names: ADRM1GP110
UniProt & NIH Common Fund Data Resources
Find proteins for Q16186 (Homo sapiens)
Explore Q16186 
Go to UniProtKB:  Q16186
PHAROS:  Q16186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16186
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XAY
Query on XAY

Download Ideal Coordinates CCD File 
B [auth A]2-{[(2S)-2-cyano-3-{3-[(4-methylbenzene-1-carbonyl)amino]phenyl}propanoyl]amino}benzoic acid
C25 H21 N3 O4
HDTWPJOTTCXUOT-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 7KXI Olderado

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-12-03 
  • Released Date: 2021-12-15 
  • Deposition Author(s): Lu, X., Walters, K.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1 ZIA BC011490
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1 ZIA BC011627

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references