8FJX

Human GAR transformylase in complex with GAR substrate and AGF320 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure-Based Design of Transport-Specific Multitargeted One-Carbon Metabolism Inhibitors in Cytosol and Mitochondria.

Nayeen, M.J.Katinas, J.M.Magdum, T.Shah, K.Wong, J.E.O'Connor, C.E.Fifer, A.N.Wallace-Povirk, A.Hou, Z.Matherly, L.H.Dann 3rd, C.E.Gangjee, A.

(2023) J Med Chem 66: 11294-11323

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00763
  • Primary Citation of Related Structures:  
    8FJT, 8FJU, 8FJV, 8FJW, 8FJX, 8FJY

  • PubMed Abstract: 

    Multitargeted agents provide tumor selectivity with reduced drug resistance and dose-limiting toxicities. We previously described the multitargeted 6-substituted pyrrolo[3,2- d ]pyrimidine antifolate 1 with activity against early- and late-stage pancreatic tumors with limited tumor selectivity. Structure-based design with our human serine hydroxymethyl transferase (SHMT) 2 and glycinamide ribonucleotide formyltransferase (GARFTase) structures, and published X-ray crystal structures of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC), SHMT1, and folate receptor (FR) α and β afforded 11 analogues. Multitargeted inhibition and selective tumor transport were designed by providing promiscuous conformational flexibility in the molecules. Metabolite rescue identified mitochondrial C1 metabolism along with de novo purine biosynthesis as the targeted pathways. We identified analogues with tumor-selective transport via FRs and increased SHMT2, SHMT1, and GARFTase inhibition (28-, 21-, and 11-fold, respectively) compared to 1 . These multitargeted agents represent an exciting new structural motif for targeted cancer therapy with substantial advantages of selectivity and potency over clinically used antifolates.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trifunctional purine biosynthetic protein adenosine-3210Homo sapiensMutation(s): 0 
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
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
Y7L (Subject of Investigation/LOI)
Query on Y7L

Download Ideal Coordinates CCD File 
B [auth A]N-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid
C21 H25 N5 O6 S
RQAHNHUMMCUWMX-AWEZNQCLSA-N
GAR
Query on GAR

Download Ideal Coordinates CCD File 
C [auth A]GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.251α = 90
b = 75.251β = 90
c = 100.037γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA250469

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release