7M3Y | pdb_00007m3y

Structure of TIM-3 in complex with 8-chloro-2-methyl-9-(3-mehtylpyridin-4-yl)-[1,2,4]triazolo[1,5-c]quinazolin-5(6H)-one (compound 22)

• PDB DOI: https://doi.org/10.2210/pdb7M3Y/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2021-03-19 Released: 2021-10-13 
• Deposition Author(s): Rietz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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

• PubMed: 34597046 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01336
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.
Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6600, United States.
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.66 kDa 
• Atom Count: 997 
• Modeled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis A virus cellular receptor 2	A [auth B]	109	Homo sapiens	Mutation(s): 0  Gene Names: HAVCR2, TIM3, TIMD3 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YQ7 (Subject of Investigation/LOI)	B	(4R,10aP)-8-chloro-2-methyl-9-(3-methylpyridin-4-yl)[1,2,4]triazolo[1,5-c]quinazolin-5(6H)-one C16 H12 Cl N5 O FVTXWRGKBOWNPA-UHFFFAOYSA-N
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.958	α = 90
b = 85.343	β = 90
c = 53.697	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-11-13
  Changes: Structure summary