7JG4

Human GAR transformylase in complex with GAR substrate and AGF131 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7JG4/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-18 Released: 2021-03-31 
• Deposition Author(s): Wong-Roushar, J., Dann III, C.E.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.255 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Discovery of 6-substituted thieno[2,3-d]pyrimidine analogs as dual inhibitors of glycinamide ribonucleotide formyltransferase and 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase in de novo purine nucleotide biosynthesis in folate receptor expressing human tumors

Wallace-Povirk, A., Tong, N., Wong-Roushar, J., O'Connor, C., Zhou, X., Hou, Z., Bao, X., Garcia, G.E., Li, J., Kim, S., Dann III, C.E., Matherly, L.H., Gangjee, A.

(2021) Bioorg Med Chem 37: 116093

• DOI: https://doi.org/10.1016/j.bmc.2021.116093

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.58 kDa 
• Atom Count: 1,596 
• Modelled Residue Count: 200 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trifunctional purine biosynthetic protein adenosine-3	A	210	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V9V (Subject of Investigation/LOI)	C [auth A]	N-(5-{3-[(1S,7R,8R,9S)-4-amino-2-oxo-7lambda~4~-thia-3,5-diazatetracyclo[4.3.0.0~1,7~.0~7,9~]nona-3,5-dien-8-yl]propyl}thiophene-2-carbonyl)-L-glutamic acid C19 H20 N4 O6 S2 VCNJYHGDMDELAI-LBPRGKRZSA-N
GAR	B [auth A]	GLYCINAMIDE RIBONUCLEOTIDE C7 H13 N2 O8 P OBQMLSFOUZUIOB-SHUUEZRQSA-L
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.255 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.278	α = 90
b = 74.278	β = 90
c = 100.344	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Wong-Roushar, J., Dann III, C.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA166711

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 2.0: 2023-10-18
  Changes: Data collection, Database references, Non-polymer description, Refinement description