8QNH

Crystal structure of the E3 ubiquitin ligase Cbl-b with an allosteric inhibitor (WO2020264398 Ex23)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Novel Benzodiazepine Series of Cbl-b Inhibitors for the Enhancement of Antitumor Immunity.

Boerth, J.A.Chinn, A.J.Schimpl, M.Bommakanti, G.Chan, C.Code, E.L.Giblin, K.A.Gohlke, A.Hansel, C.S.Jin, M.Kavanagh, S.L.Lamb, M.L.Lane, J.S.Larner, C.J.B.Mfuh, A.M.Moore, R.K.Puri, T.Quinn, T.R.Ye, M.Robbins, K.J.Gancedo-Rodrigo, M.Tang, H.Walsh, J.Ware, J.Wrigley, G.L.Reddy, I.K.Zhang, Y.Grimster, N.P.

(2023) ACS Med Chem Lett 14: 1848-1856

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00439
  • Primary Citation of Related Structures:  
    8QNG, 8QNH, 8QNI

  • PubMed Abstract: 

    Casitas B-lineage lymphoma proto-oncogene-b (Cbl-b) is a RING finger E3 ligase that is responsible for repressing T-cell, natural killer (NK) cell, and B-cell activation. The robust antitumor activity observed in Cbl-b deficient mice arising from elevated T-cell and NK-cell activity justified our discovery effort toward Cbl-b inhibitors that might show therapeutic promise in immuno-oncology, where activation of the immune system can drive the recognition and killing of cancer cells. We undertook a high-throughput screening campaign followed by structure-enabled optimization to develop a novel benzodiazepine series of potent Cbl-b inhibitors. This series displayed nanomolar levels of biochemical potency, as well as potent T-cell activation. The functional activity of this class of Cbl-b inhibitors was further corroborated with ubiquitin-based cellular assays.


  • Organizational Affiliation

    Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CBL-B394Homo sapiensMutation(s): 0 
Gene Names: CBLB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13191 (Homo sapiens)
Explore Q13191 
Go to UniProtKB:  Q13191
PHAROS:  Q13191
GTEx:  ENSG00000114423 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z3N (Subject of Investigation/LOI)
Query on Z3N

Download Ideal Coordinates CCD File 
B [auth A]2-{3-[(1s,3R)-3-methyl-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(3S)-3-methylpiperidin-1-yl]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one
C30 H34 F3 N5 O
HUOLMBXGHHSYHC-QWQFASRJSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.04α = 90
b = 73.594β = 90
c = 93.973γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
STARANISOdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-11-22 
  • Deposition Author(s): Schimpl, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2024-01-03
    Changes: Database references