8JUB

Crystal structure of glutaminase C in complex with compound 27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting the Subpocket Enables the Discovery of Thiadiazole-Pyridazine Derivatives as Glutaminase C Inhibitors.

Sun, H.Du, T.Yang, M.Liu, X.Xue, X.Chen, K.Lang, X.Chen, X.Wang, B.Wang, X.

(2023) ACS Med Chem Lett 14: 1455-1466

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00375
  • Primary Citation of Related Structures:  
    8JUB, 8JUE

  • PubMed Abstract: 

    As glutaminase C (GAC) has become an attractive target for cancer treatment by regulating glutaminolysis, thus, interest in GAC inhibitors has risen in recent years. Herein, a potential binding subpocket comprising basic residues was identified, and through extensive structure-activity relationship studies, promising inhibitors 11 and 39 were identified with robust GAC inhibitory activity and A549 cell antiproliferative activity. X-ray crystallography of the 11 -GAC and 27 -GAC complexes revealed a novel binding mode against GAC. The potency of 11 and 27 against GAC K320A further highlighted the importance of the binding. Notably, compounds 11 and 39 regulated the cellular metabolite, thereby increasing reactive oxygen species by blocking glutamine metabolism. Compound 11 also exhibited excellent antiproliferative activity in the A549 cell xenograft model. We further proved that 11 is a safe GAC allosteric inhibitor. A basic subpocket is proposed that might provide new strategies for the development of novel GAC inhibitors in the future.


  • Organizational Affiliation

    State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrial
A, B, C, D
533Homo sapiensMutation(s): 0 
Gene Names: GLSGLS1KIAA0838
EC: 3.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O94925 (Homo sapiens)
Explore O94925 
Go to UniProtKB:  O94925
PHAROS:  O94925
GTEx:  ENSG00000115419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94925
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V4I
Query on V4I

Download Ideal Coordinates CCD File 
E [auth A],
F [auth D]
3-[2-oxidanylidene-2-[[5-[[(3R)-1-pyridazin-3-ylpyrrolidin-3-yl]amino]-1,3,4-thiadiazol-2-yl]amino]ethyl]benzoic acid
C19 H19 N7 O3 S
HMCXTWYQJBJKRJ-CQSZACIVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.479α = 90
b = 138.71β = 93.09
c = 178.425γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)United KingdomCIFMS, No. 2021-I2M-1-028

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references