8GCY | pdb_00008gcy

Co-crystal structure of CBL-B in complex with N-Aryl isoindolin-1-one inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8GCY/pdb

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


• Deposited: 2023-03-03 Released: 2023-03-22 
• Deposition Author(s): Kimani, S., Zeng, H., Dong, A., Li, Y., Santhakumar, V., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.230 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition.

Kimani, S.W., Perveen, S., Szewezyk, M., Zeng, H., Dong, A., Li, F., Ghiabi, P., Li, Y., Chau, I., Arrowsmith, C.H., Barsyte-Lovejoy, D., Santhakumar, V., Vedadi, M., Halabelian, L.

(2023) Commun Biol 6: 1272-1272

• PubMed: 38104184 
• DOI: https://doi.org/10.1038/s42003-023-05655-8
• Primary Citation Related Structures: 
  8GCY


• PubMed Abstract: 
  

  Cbl-b is a RING-type E3 ubiquitin ligase that is expressed in several immune cell lineages, where it negatively regulates the activity of immune cells. Cbl-b has specifically been identified as an attractive target for cancer immunotherapy due to its role in promoting an immunosuppressive tumor environment. A Cbl-b inhibitor, Nx-1607, is currently in phase I clinical trials for advanced solid tumor malignancies. Using a suite of biophysical and cellular assays, we confirm potent binding of C7683 (an analogue of Nx-1607) to the full-length Cbl-b and its N-terminal fragment containing the TKBD-LHR-RING domains. To further elucidate its mechanism of inhibition, we determined the co-crystal structure of Cbl-b with C7683, revealing the compound's interaction with both the TKBD and LHR, but not the RING domain. Here, we provide structural insights into a novel mechanism of Cbl-b inhibition by a small-molecule inhibitor that locks the protein in an inactive conformation by acting as an intramolecular glue.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada. [e-mail].
Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.98 kDa 
• Atom Count: 3,233 
• Modeled Residue Count: 376 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL-B	A	391	Homo sapiens	Mutation(s): 0  Gene Names: CBLB, RNF56, Nbla00127 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z3N (Subject of Investigation/LOI)	D [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
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	G [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
Z3N	BindingDB:  8GCY	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: 1.81 Å
• R-Value Free:  0.230 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.937	α = 90
b = 76.093	β = 90
c = 105.464	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Kimani, S., Zeng, H., Dong, A., Li, Y., Santhakumar, V., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Database references