5FI2

Crystal structure of human GAC in complex with inhibitor UPGL_00009: 2-phenyl-~{N}-[5-[[(3~{R})-1-[5-(2-phenylethanoylamino)-1,3,4-thiadiazol- 2-yl]pyrrolidin-3-yl]amino]-1,3,4-thiadiazol-2-yl]ethanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 10.1016/j.bmc.2016.03.009
  • Primary Citation of Related Structures:  
    5I94, 5FI2, 5FI7, 5FI6

  • 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 ...

    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

    Cornell University, Department of Molecular Medicine, Ithaca, NY 14853, USA; Cornell University, Department of Chemistry and Chemical Biology, Ithaca, NY 14853, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutaminase kidney isoform, mitochondrialA, B, C, D539Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5XX (Subject of Investigation/LOI)
Query on 5XX

Download Ideal Coordinates CCD File 
E [auth A], F [auth D]2-phenyl-~{N}-[5-[[(3~{R})-1-[5-(2-phenylethanoylamino)-1,3,4-thiadiazol-2-yl]pyrrolidin-3-yl]amino]-1,3,4-thiadiazol-2-yl]ethanamide
C24 H24 N8 O2 S2
XKAUHJUBYCZSGD-GOSISDBHSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5XX BindingDB:  5FI2 IC50: min: 14, max: 30 (nM) from 2 assay(s)
Binding MOAD:  5FI2 IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.054α = 90
b = 138.618β = 90
c = 176.313γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-22 
  • Released Date: 2016-05-11 
  • Deposition Author(s): Huang, Q., Cerione, R.

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