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 4ZZ2 | pdb_00004zz2

HUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR AND (S)-2-({5-[3-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-PROPYL]-THIOPHENE-3-CARBONYL}-AMINO)-PENTANEDIOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.162 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4ZZ2

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.5b00801
  • Primary Citation Related Structures: 
    4ZZ1, 4ZZ2, 4ZZ3

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 23.54 kDa 
  • Atom Count: 1,929 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trifunctional purine biosynthetic protein adenosine-3210Homo sapiensMutation(s): 0 
Gene Names: GART, PGFT, PRGS
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
GTEx:  ENSG00000159131 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22102
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3YG

Query on 3YG



Download:Ideal Coordinates CCD File
C [auth A](S)-2-({5-[3-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)-propyl]-thiophene-3-carbonyl}-amino)-pentanedioic acid
C19 H21 N5 O6 S
RMEHPWHLFJJYTB-ZDUSSCGKSA-N
GAR

Query on GAR



Download:Ideal Coordinates CCD File
B [auth A]GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
3YG BindingDB:  4ZZ2 Ki: 9.1 (nM) from 1 assay(s)
IC50: 2.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.162 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.577α = 90
b = 75.577β = 90
c = 100.995γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report



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 StatesGM094472
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA166711

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description