10ZJ | pdb_000010zj

Structure of Cbl-B bound to compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 10ZJ

This is version 1.0 of the entry. See complete history

Literature

Optimization and In Vivo Characterization of a Series of Cbl‐b Inactive-State Inhibitors.

Lambrecht, M.J.Liang, J.Ung, P.M.Huestis, M.P.Zhu, B.Y.Barton, L.M.Castanedo, G.M.Zbieg, J.R.Larouche-Gauthier, R.Jakalian, A.Leclerc, J.P.Yadav, A.Haghshenas, P.Aubert-Nicol, S.Ismaili, H.Zhao, L.Leblanc, M.Wang, J.Wang, S.Wang, Q.Garner, T.Tan, S.Prangley, M.Broccatelli, F.Pang, J.Murray, J.Yu, C.Hsu, P.Rutz, S.Kakiuchi-Kiyota, S.Ishizuka, I.Leung, D.H.Kou, P.Bao, L.Wang, X.

(2026) ACS Med Chem Lett 17: 1253-1257

  • DOI: https://doi.org/10.1021/acsmedchemlett.6c00103
  • Primary Citation Related Structures: 
    10ZJ

  • PubMed Abstract: 

    Casitas B-lineage lymphoma-b (Cbl-b), an E3 ubiquitin ligase, is a key negative regulator of immune function, and its inhibition is a promising strategy for cancer immunotherapy. Here, we show the optimization of a series of inactive-state Cbl-b inhibitors to improve their potency and pharmacokinetic properties. Through systematic modification of a benzylic amine and a linker region, compound 16 was identified, which demonstrates a favorable balance of biochemical potency, cellular activity, and in vitro ADME properties. Despite exhibiting high IV clearance in vivo , compound 16 achieved oral exposures sufficient to demonstrate significant tumor growth inhibition in a murine CT26 colon-cancer model.


  • Organizational Affiliation
    • Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 48.64 kDa 
  • Atom Count: 3,570 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 410 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CBL-B410Homo sapiensMutation(s): 1 
Gene Names: CBLBRNF56Nbla00127
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13191
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1DCC(
Subject of Investigation/LOI)

Query on A1DCC



Download:Ideal Coordinates CCD File
G [auth A]6-{[(3,3-difluoropropyl)amino]methyl}-2-(3-{3-[(R)-fluoro(4-methyl-4H-1,2,4-triazol-3-yl)methyl]oxetan-3-yl}phenyl)-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one
C26 H25 F6 N5 O2
KGRGPZLKLFGPCN-QFIPXVFZSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.19α = 90
b = 74.12β = 90
c = 97.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release