5FI7

Crystal structure of human GAC in complex with inhibitor UPGL_00015: 2-phenyl-~{N}-[5-[(3~{S})-3-[[5-(2-phenylethanoylamino)-1,3,4-thiadiazol-2-yl]oxy]pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl]ethanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and evaluation of novel glutaminase inhibitors.

McDermott, L.A.Iyer, P.Vernetti, L.Rimer, S.Sun, J.Boby, M.Yang, T.Fioravanti, M.O'Neill, J.Wang, L.Drakes, D.Katt, W.Huang, Q.Cerione, R.

(2016) Bioorg Med Chem 24: 1819-1839

  • DOI: https://doi.org/10.1016/j.bmc.2016.03.009
  • Primary Citation of Related Structures:  
    5FI2, 5FI6, 5FI7, 5I94

  • PubMed Abstract: 

    A novel set of GAC (kidney glutaminase isoform C) inhibitors able to inhibit the enzymatic activity of GAC and the growth of the triple negative MDA-MB-231 breast cancer cells with low nanomolar potency is described. Compounds in this series have a reduced number of rotatable bonds, improved ClogPs, microsomal stability and ligand efficiency when compared to the leading GAC inhibitors BPTES and CB-839. Property improvements were achieved by the replacement of the flexible n-diethylthio or the n-butyl moiety present in the leading inhibitors by heteroatom substituted heterocycloalkanes.


  • Organizational Affiliation

    University of Pittsburgh, Department of Pharmaceutical Sciences, Pittsburgh, PA 15261, USA; University of Pittsburgh, Drug Discovery Institute, Pittsburgh, PA 15261, USA. Electronic address: lam179@pitt.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrial
A, B, C, D
539Homo sapiensMutation(s): 0 
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
5XZ
Query on 5XZ

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
2-phenyl-~{N}-[5-[(3~{S})-3-[[5-(2-phenylethanoylamino)-1,3,4-thiadiazol-2-yl]oxy]pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl]ethanamide
C24 H23 N7 O3 S2
JGTIIKRXHSZCBG-SFHVURJKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5XZ BindingDB:  5FI7 IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.174α = 90
b = 138.829β = 90
c = 176.653γ = 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: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description