8QNH | pdb_00008qnh

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

• PDB DOI: https://doi.org/10.2210/pdb8QNH/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-26 Released: 2023-11-22 
• Deposition Author(s): Schimpl, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

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

• PubMed: 38116444 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00439
• Primary Citation 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.

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Organizational Affiliation: 
• Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States.
Discovery Sciences, R&D, The Discovery Centre, AstraZeneca, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom.
Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States.
DMPK, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom.
Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States.
Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Biomedical Campus, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom.
Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom.
High Throughput Screening, Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.5 kDa 
• Atom Count: 3,171 
• Modeled Residue Count: 384 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL-B	A	394	Homo sapiens	Mutation(s): 0  Gene Names: CBLB EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13191 (Homo sapiens) Explore Q13191  Go to UniProtKB:  Q13191
PHAROS:  Q13191 GTEx:  ENSG00000114423

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z3N (Subject of Investigation/LOI)	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	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z3N	BindingDB:  8QNH	Kd: min: 3, max: 8 (nM) from 2 assay(s)
		IC50: min: 5, max: 9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.04	α = 90
b = 73.594	β = 90
c = 93.973	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
STARANISO	data scaling
XDS	data reduction
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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