4ZZ3

Human GAR transformylase in complex with GAR and pemetrexed


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Regioisomers as Targeted Antifolates for Folate Receptor alpha and the Proton-Coupled Folate Transporter in Human Tumors.

Wang, L.Wallace, A.Raghavan, S.Deis, S.M.Wilson, M.R.Yang, S.Polin, L.White, K.Kushner, J.Orr, S.George, C.O'Connor, C.Hou, Z.Mitchell-Ryan, S.Dann, C.E.Matherly, L.H.Gangjee, A.

(2015) J.Med.Chem. 58: 6938-6959

  • DOI: 10.1021/acs.jmedchem.5b00801
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2-Amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine antifolate thiophene regioisomers of AGF94 (4) with a thienoyl side chain and three-carbon bridge lengths [AGF150 (5) and AGF154 (7)] were synthesized as potential antitumor agents. These analogues ...

    2-Amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine antifolate thiophene regioisomers of AGF94 (4) with a thienoyl side chain and three-carbon bridge lengths [AGF150 (5) and AGF154 (7)] were synthesized as potential antitumor agents. These analogues inhibited proliferation of Chinese hamster ovary (CHO) sublines expressing folate receptors (FRs) α or β (IC50s < 1 nM) or the proton-coupled folate transporter (PCFT) (IC50 < 7 nM). Compounds 5 and 7 inhibited KB, IGROV1, and SKOV3 human tumor cells at subnanomolar concentrations, reflecting both FRα and PCFT uptake. AGF152 (6) and AGF163 (8), 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine thiophene regioisomers, also inhibited growth of FR-expressing CHO and KB cells. All four analogues inhibited glycinamide ribonucleotide formyltransferase (GARFTase). Crystal structures of human GARFTase complexed with 5 and 7 were reported. In severe combined immunodeficient mice bearing SKOV3 tumors, 7 was efficacious. The selectivity of these compounds for PCFT and for FRα and β over the ubiquitously expressed reduced folate carrier is a paradigm for selective tumor targeting.


    Organizational Affiliation

    Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trifunctional purine biosynthetic protein adenosine-3
A
210Homo sapiensMutation(s): 0 
Gene Names: GART (PGFT, PRGS)
Find proteins for P22102 (Homo sapiens)
Go to Gene View: GART
Go to UniProtKB:  P22102
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4DW
Query on 4DW

Download SDF File 
Download CCD File 
A
N-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid
pemetrexed
C20 H19 N5 O6
OOPGILDDKAKTLT-GWJCSSMESA-N
 Ligand Interaction
GAR
Query on GAR

Download SDF File 
Download CCD File 
A
GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4DWKi: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.983α = 90.00
b = 74.983β = 90.00
c = 100.934γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing

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 StatesGM094472
National Institutes of Health/National Cancer InstituteUnited StatesCA166711

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.2: 2018-06-13
    Type: Data collection