7M41

Structure of TIM-3 in complex with N-(4-(8-chloro-2-methyl-5-oxo-5,6-dihydro-[1,2,4]traizolo[1,5-c]quinazolin-9-yl)-3-methylphenyl)-1H-imidazole-2-sulfonamide (compound 38)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of Small Molecules Bound to T-Cell Immunoglobulin and Mucin Domain-Containing Molecule 3 (TIM-3).

Rietz, T.A.Teuscher, K.B.Mills, J.J.Gogliotti, R.D.Lepovitz, L.T.Scaggs, W.R.Yoshida, K.Luong, K.Lee, T.Fesik, S.W.

(2021) J Med Chem 64: 14757-14772

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01336
  • Primary Citation of Related Structures:  
    7M3Y, 7M3Z, 7M41

  • PubMed Abstract: 

    T-cell immunoglobulin and mucin domain-containing molecule 3 (TIM-3; HAVCR2) has emerged as an attractive immune checkpoint target for cancer immunotherapy. TIM-3 is a negative regulator of the systemic immune response to cancer and is expressed on several dysfunctional, or exhausted, immune cell subsets. Upregulation of TIM-3 is associated with tumor progression, poor survival rates, and acquired resistance to antibody-based immunotherapies in the clinic. Despite the potential advantages of small-molecule inhibitors over antibodies, the discovery of small-molecule inhibitors has lagged behind that of antibody therapeutics. Here, we describe the discovery of high-affinity small-molecule ligands for TIM-3 through an NMR-based fragment screen and structure-based lead optimization. These compounds represent useful tools to further study the biology of TIM-3 immune modulation in cancer and serve as a potentially useful starting point toward the discovery of TIM-3-targeted therapeutics.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatitis A virus cellular receptor 2
A, B
109Homo sapiensMutation(s): 0 
Gene Names: HAVCR2TIM3TIMD3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDQ0 (Homo sapiens)
Explore Q8TDQ0 
Go to UniProtKB:  Q8TDQ0
PHAROS:  Q8TDQ0
GTEx:  ENSG00000135077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.215α = 90
b = 46.828β = 93.05
c = 53.905γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-10-13 
  • Deposition Author(s): Rietz, T.A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description