9FQH

E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Accelerated Discovery of Carbamate Cbl-b Inhibitors Using Generative AI Models and Structure-Based Drug Design.

Quinn, T.R.Giblin, K.A.Thomson, C.Boerth, J.A.Bommakanti, G.Braybrooke, E.Chan, C.Chinn, A.J.Code, E.Cui, C.Fan, Y.Grimster, N.P.Kohara, K.Lamb, M.L.Ma, L.Mfuh, A.M.Robb, G.R.Robbins, K.J.Schimpl, M.Tang, H.Ware, J.Wrigley, G.L.Xue, L.Zhang, Y.Zhu, H.Hughes, S.J.

(2024) J Med Chem 67: 14210-14233

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01034
  • Primary Citation of Related Structures:  
    9FQH, 9FQI, 9FQJ

  • PubMed Abstract: 

    Casitas B-lymphoma proto-oncogene-b (Cbl-b) is a RING finger E3 ligase that has an important role in effector T cell function, acting as a negative regulator of T cell, natural killer (NK) cell, and B cell activation. A discovery effort toward Cbl-b inhibitors was pursued in which a generative AI design engine, REINVENT, was combined with a medicinal chemistry structure-based design to discover novel inhibitors of Cbl-b. Key to the success of this effort was the evolution of the "Design" phase of the Design-Make-Test-Analyze cycle to involve iterative rounds of an in silico structure-based drug design, strongly guided by physics-based affinity prediction and machine learning DMPK predictive models, prior to selection for synthesis. This led to the accelerated discovery of a potent series of carbamate Cbl-b inhibitors.


  • Organizational Affiliation

    Early TDE Discovery, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, 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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IEW (Subject of Investigation/LOI)
Query on A1IEW

Download Ideal Coordinates CCD File 
B [auth A]8-[3-[3-methyl-1-(4-methyl-1,2,4-triazol-3-yl)cyclobutyl]phenyl]-3-[[(3~{S})-3-methylpiperidin-1-yl]methyl]-5-(trifluoromethyl)-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one
C28 H32 F3 N7 O
MIDJBXBDZRDWNR-RWYJCYHVSA-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: 1.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.811α = 90
b = 73.873β = 90
c = 93.608γ = 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: 2024-07-31 
  • Deposition Author(s): Schimpl, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references