10YS | pdb_000010ys

Structure of Cbl-B bound to compound 33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 10YS

This is version 1.0 of the entry. See complete history

Literature

Optimization Leading to a Potent and Selective Cbl‐b Inactive-State Inhibitor That Demonstrated In Vivo Efficacy.

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

(2026) ACS Med Chem Lett 17: 1258-1265

  • DOI: https://doi.org/10.1021/acsmedchemlett.6c00104
  • Primary Citation Related Structures: 
    10YS, 10ZF

  • PubMed Abstract: 

    In the preceding work in this issue (10.1021/acsmedchemlett.6c00103), we described our initial structure-activity relationship (SAR) optimization that led to a pan-Cbl inhibitor ( 6 ) that demonstrated efficacy in a mouse CT26 syngeneic model. Unfortunately, attempts to improve TGI with higher doses of 6 resulted in poor tolerability which we attributed to a lack of selectivity between Cbl-b and c-Cbl (∼2× by surface plasmon resonance (SPR)). Herein, we report our continued efforts that led to a breakthrough in achieving Cbl-b selectivity (up to 37×). The lead compound 33 demonstrated 14× selectivity against c-Cbl by SPR, was potent in a PBMC cell assay, and showed good oral exposure in mice. When tested in a CT26 model, 33 displayed improved tumor growth inhibition compared to our previously reported pan-Cbl inhibitor 6 (TGI 145% vs 82%). More importantly, 33 was better tolerated than 6 , supporting our hypothesis that a selective Cbl-b inhibitor could be advantageous relative to a pan-Cbl inhibitor.


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

Macromolecule Content 

  • Total Structure Weight: 98.59 kDa 
  • Atom Count: 6,527 
  • Modeled Residue Count: 769 
  • Deposited Residue Count: 820 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase CBL-B
A, B
410Homo 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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1DCD(
Subject of Investigation/LOI)

Query on A1DCD



Download:Ideal Coordinates CCD File
O [auth A],
Y [auth B]
2-{3-[(1r,3r)-3-methoxy-1-(4-methyl-4H-1,2,4-triazol-3-yl)cyclobutyl]phenyl}-6-{[(1-methylcyclobutyl)amino]methyl}-4-(trifluoromethyl)-2,3-dihydro-1H-isoindol-1-one
C29 H32 F3 N5 O2
GXSZEJJGRAAVEG-BFZJZIARSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
T [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
Q [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
U [auth B],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



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

Query on MG



Download:Ideal Coordinates CCD File
L [auth A],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.275α = 90
b = 74.032β = 93.68
c = 106.8γ = 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