7JG3 | pdb_00007jg3

Human GAR transformylase in complex with GAR substrate and AGF103 inhibitor

PDB DOI: https://doi.org/10.2210/pdb7JG3/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.187 (Depositor), 0.189 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7JG3

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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, C.E., Matherly, L.H., Gangjee, A.

(2021) Bioorg Med Chem 37: 116093

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

Macromolecule Content

Total Structure Weight: 23.58 kDa
Atom Count: 1,699
Modeled Residue Count: 200
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22102
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V9A (Subject of Investigation/LOI) Query on V9A Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-{5-[4-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]furan-2-carbonyl}-L-glutamic acid C₂₀ H₂₂ N₄ O₇ S LYDGQYDYRQVOBF-ZDUSSCGKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GAR Query on GAR Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCINAMIDE RIBONUCLEOTIDE C₇ H₁₃ N₂ O₈ P OBQMLSFOUZUIOB-SHUUEZRQSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.187 (Depositor), 0.189 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.522	α = 90
b = 74.522	β = 90
c = 100.06	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Wong-Roushar, J.

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

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.