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: 2.44 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1074/jbc.M117.810101
  • Primary Citation of Related Structures:  
    5WJ6

  • 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 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

    From the Cornell High Energy Synchrotron Source (CHESS) and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrial
A, C, D
539Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrial539Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B4A
Query on B4A

Download Ideal Coordinates CCD File 
E [auth A],
F [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.652α = 90
b = 138.01β = 90
c = 175.769γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM040654
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM047458
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM061762

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2018-03-21
    Changes: Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description