5WJ6

Crystal structure of glutaminase C in complex with inhibitor 2-phenyl-N-{5-[4-({5-[(phenylacetyl)amino]-1,3,4-thiadiazol-2-yl}amino)piperidin-1-yl]-1,3,4-thiadiazol-2-yl}acetamide (UPGL-00004)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.445 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Characterization of the interactions of potent allosteric inhibitors with glutaminase C, a key enzyme in cancer cell glutamine metabolism.

Huang, Q.Stalnecker, C.Zhang, C.McDermott, L.A.Iyer, P.O'Neill, J.Reimer, S.Cerione, R.A.Katt, W.P.

(2018) J. Biol. Chem. 293: 3535-3545

  • DOI: 10.1074/jbc.M117.810101

  • PubMed Abstract: 
  • Altered glycolytic flux in cancer cells (the "Warburg effect") causes their proliferation to rely upon elevated glutamine metabolism ("glutamine addiction"). This requirement is met by the overexpression of glutaminase C (GAC), which catalyzes the fi ...

    Altered glycolytic flux in cancer cells (the "Warburg effect") causes their proliferation to rely upon elevated glutamine metabolism ("glutamine addiction"). This requirement is met by the overexpression of glutaminase C (GAC), which catalyzes the first step in glutamine metabolism and therefore represents a potential therapeutic target. The small molecule CB-839 was reported to be more potent than other allosteric GAC inhibitors, including the parent compound bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl)ethyl (BPTES), and is in clinical trials. Recently, we described the synthesis of BPTES analogs having distinct saturated heterocyclic cores as a replacement for the flexible chain moiety, with improved microsomal stability relative to CB-839 and BPTES. Here, we show that one of these new compounds, UPGL00004, like CB-839, more potently inhibits the enzymatic activity of GAC, compared with BPTES. We also compare the abilities of UPGL00004, CB-839, and BPTES to directly bind to recombinant GAC and demonstrate that UPGL00004 has a similar binding affinity as CB-839 for GAC. We also show that UPGL00004 potently inhibits the growth of triple-negative breast cancer cells, as well as tumor growth when combined with the anti-vascular endothelial growth factor antibody bevacizumab. Finally, we compare the X-ray crystal structures for UPGL00004 and CB-839 bound to GAC, verifying that UPGL00004 occupies the same binding site as CB-839 or BPTES and that all three inhibitors regulate the enzymatic activity of GAC via a similar allosteric mechanism. These results provide insights regarding the potency of these inhibitors that will be useful in designing novel small-molecules that target a key enzyme in cancer cell metabolism.


    Organizational Affiliation

    Molecular Medicine, Cornell University, Ithaca, New York 14853 and.,From the Cornell High Energy Synchrotron Source (CHESS) and.,Departments of Chemistry and Chemical Biology and.,From the Cornell High Energy Synchrotron Source (CHESS) and rac1@cornell.edu.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Department of Pharmaceutical Sciences and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaminase kidney isoform, mitochondrial
A, C, D
539Homo sapiensMutation(s): 0 
Gene Names: GLS (GLS1, KIAA0838)
EC: 3.5.1.2
Find proteins for O94925 (Homo sapiens)
Go to Gene View: GLS
Go to UniProtKB:  O94925
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutaminase kidney isoform, mitochondrial
B
539Homo sapiensMutation(s): 0 
Gene Names: GLS (GLS1, KIAA0838)
EC: 3.5.1.2
Find proteins for O94925 (Homo sapiens)
Go to Gene View: GLS
Go to UniProtKB:  O94925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B4A
Query on B4A

Download SDF File 
Download CCD File 
A, C
2-phenyl-N-{5-[4-({5-[(phenylacetyl)amino]-1,3,4-thiadiazol-2-yl}amino)piperidin-1-yl]-1,3,4-thiadiazol-2-yl}acetamide
C25 H26 N8 O2 S2
MRYCNTHLPRENBA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.445 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.652α = 90.00
b = 138.010β = 90.00
c = 175.769γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM040654
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM047458
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM061762

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Database references
  • Version 1.3: 2018-03-21
    Type: Database references