8FE0 | pdb_00008fe0

Human GAR transformylase in complex with GAR substrate and AGF305 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Multitargeted 6-Substituted Thieno[2,3- d ]pyrimidines as Folate Receptor-Selective Anticancer Agents that Inhibit Cytosolic and Mitochondrial One-Carbon Metabolism.

Tong, N.Wong-Roushar, J.Wallace-Povirk, A.Shah, Y.Nyman, M.C.Katinas, J.M.Schneider, M.O'Connor, C.Bao, X.Kim, S.Li, J.Hou, Z.Matherly, L.H.Dann 3rd, C.E.Gangjee, A.

(2023) Acs Pharmacol Transl Sci 6: 748-770

  • DOI: https://doi.org/10.1021/acsptsci.3c00020
  • Primary Citation Related Structures: 
    8FDX, 8FDY, 8FE0, 9NX6

  • PubMed Abstract: 

    Multitargeted agents with tumor selectivity result in reduced drug resistance and dose-limiting toxicities. We report 6-substituted thieno[2,3- d ]pyrimidine compounds ( 3 - 9 ) with pyridine ( 3 , 4 ), fluorine-substituted pyridine ( 5 ), phenyl ( 6 , 7 ), and thiophene side chains ( 8 , 9 ), for comparison with unsubstituted phenyl ( 1 , 2 ) and thiophene side chain ( 10 , 11 ) containing thieno[2,3- d ]pyrimidine compounds. Compounds 3 - 9 inhibited proliferation of Chinese hamster ovary cells (CHO) expressing folate receptors (FRs) α or β but not the reduced folate carrier (RFC); modest inhibition of CHO cells expressing the proton-coupled folate transporter (PCFT) by 4 , 5 , 6 , and 9 was observed. Replacement of the side-chain 1',4'-phenyl ring with 2',5'-pyridyl, or 2',5'-pyridyl with a fluorine insertion ortho to l-glutamate resulted in increased potency toward FR-expressing CHO cells. Toward KB tumor cells, 4 - 9 were highly active (IC 50 's from 2.11 to 7.19 nM). By metabolite rescue in KB cells and in vitro enzyme assays, de novo purine biosynthesis was identified as a targeted pathway (at 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFTase) and glycinamide ribonucleotide formyltransferase (GARFTase)). Compound 9 was 17- to 882-fold more potent than previously reported compounds 2 , 10 , and 11 against GARFTase. By targeted metabolomics and metabolite rescue, 1 , 2 , and 6 also inhibited mitochondrial serine hydroxymethyl transferase 2 (SHMT2); enzyme assays confirmed inhibition of SHMT2. X-ray crystallographic structures were obtained for 4 , 5 , 9 , and 10 with human GARFTase. This series affords an exciting new structural platform for potent multitargeted antitumor agents with FR transport selectivity.


  • Organizational Affiliation
    • Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.

Macromolecule Content 

  • Total Structure Weight: 23.53 kDa 
  • Atom Count: 1,661 
  • 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
Phosphoribosylglycinamide formyltransferase210Homo sapiensMutation(s): 0 
Gene Names: GARTPGFTPRGS
EC: 2.1.2.2 (UniProt), 6.3.4.13 (UniProt), 6.3.3.1 (UniProt)
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
XSO
(Subject of Investigation/LOI)

Query on XSO



Download:Ideal Coordinates CCD File
C [auth A]N-{5-[4-(2-amino-4-oxo-1,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]-3-fluoropyridine-2-carbonyl}-L-glutamic acid
C21 H22 F N5 O6 S
USGRXMVHCFOWQP-AWEZNQCLSA-N
GAR

Query on GAR



Download:Ideal Coordinates CCD File
B [auth A]GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.879α = 90
b = 74.879β = 90
c = 100.616γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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 StatesR01 CA166711
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA250469

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection