5J9F

Human GAR transformylase in complex with GAR and (4-{[2-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)ethyl]amino}benzoyl)-L-glutamic acid (AGF183)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Tumor Targeting with Novel 6-Substituted Pyrrolo [2,3-d] Pyrimidine Antifolates with Heteroatom Bridge Substitutions via Cellular Uptake by Folate Receptor alpha and the Proton-Coupled Folate Transporter and Inhibition of de Novo Purine Nucleotide Biosynthesis.

Golani, L.K.Wallace-Povirk, A.Deis, S.M.Wong, J.Ke, J.Gu, X.Raghavan, S.Wilson, M.R.Li, X.Polin, L.de Waal, P.W.White, K.Kushner, J.O'Connor, C.Hou, Z.Xu, H.E.Melcher, K.Dann, C.E.Matherly, L.H.Gangjee, A.

(2016) J Med Chem 59: 7856-7876

  • DOI: 10.1021/acs.jmedchem.6b00594
  • Primary Citation of Related Structures:  
    5IZQ, 5J9F

  • PubMed Abstract: 
  • Targeted antifolates with heteroatom replacements of the carbon vicinal to the phenyl ring in 1 by N (4), O (8), or S (9), or with N-substituted formyl (5), acetyl (6), or trifluoroacetyl (7) moieties, were synthesized and tested for selective cellular uptake by folate receptor (FR) α and β or the proton-coupled folate transporter ...

    Targeted antifolates with heteroatom replacements of the carbon vicinal to the phenyl ring in 1 by N (4), O (8), or S (9), or with N-substituted formyl (5), acetyl (6), or trifluoroacetyl (7) moieties, were synthesized and tested for selective cellular uptake by folate receptor (FR) α and β or the proton-coupled folate transporter. Results show increased in vitro antiproliferative activity toward engineered Chinese hamster ovary cells expressing FRs by 4-9 over the CH2 analogue 1. Compounds 4-9 inhibited de novo purine biosynthesis and glycinamide ribonucleotide formyltransferase (GARFTase). X-ray crystal structures for 4 with FRα and GARFTase showed that the bound conformations of 4 required flexibility for attachment to both FRα and GARFTase. In mice bearing IGROV1 ovarian tumor xenografts, 4 was highly efficacious. Our results establish that heteroatom substitutions in the 3-atom bridge region of 6-substituted pyrrolo[2,3-d]pyrimidines related to 1 provide targeted antifolates that warrant further evaluation as anticancer agents.


    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trifunctional purine biosynthetic protein adenosine-3A210Homo sapiensMutation(s): 1 
Gene Names: GARTPGFTPRGS
EC: 6.3.4.13 (PDB Primary Data), 6.3.3.1 (PDB Primary Data), 2.1.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P22102 (Homo sapiens)
Explore P22102 
Go to UniProtKB:  P22102
PHAROS:  P22102
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
83A (Subject of Investigation/LOI)
Query on 83A

Download Ideal Coordinates CCD File 
C [auth A]N-(4-{[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)ethyl]amino}benzene-1-carbonyl)-L-glutamic acid
C20 H22 N6 O6
UFNWIIALSMNORN-AWEZNQCLSA-N
 Ligand Interaction
GAR (Subject of Investigation/LOI)
Query on GAR

Download Ideal Coordinates CCD File 
B [auth A]GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
83A Binding MOAD:  5J9F Ki: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.386α = 90
b = 75.386β = 90
c = 101.293γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA166711
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094472

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence