5UY8

Crystal structure of AICARFT bound to an antifolate

PDB DOI: https://doi.org/10.2210/pdb5UY8/pdb

Classification: TRANSFERASE, HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-23 Released: 2018-01-10
Deposition Author(s): Wang, J., Wang, Y., Fales, K.R., Atwell, S., Clawson, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.245
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of N-(6-Fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)-5-[(3R)-3-hydroxypyrrolidin-1-yl]thiophene-2-sulfonamide (LSN 3213128), a Potent and Selective Nonclassical Antifolate Aminoimidazole-4-carboxamide Ribonucleotide Formyltransferase (AICARFT) Inhibitor Effective at Tumor Suppression in a Cancer Xenograft Model.

Fales, K.R., Njoroge, F.G., Brooks, H.B., Thibodeaux, S., Torrado, A., Si, C., Toth, J.L., Mc Cowan, J.R., Roth, K.D., Thrasher, K.J., Frimpong, K., Lee, M.R., Dally, R.D., Shepherd, T.A., Durham, T.B., Margolis, B.J., Wu, Z., Wang, Y., Atwell, S., Wang, J., Hui, Y.H., Meier, T.I., Konicek, S.A., Geeganage, S.

(2017) J Med Chem 60: 9599-9616

PubMed: 29072452 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.7b01046
Primary Citation of Related Structures:
5UY8, 5UZ0

PubMed Abstract:
A hallmark of cancer is unbridled proliferation that can result in increased demand for de novo synthesis of purine and pyrimidine bases required for DNA and RNA biosynthesis. These synthetic pathways are frequently upregulated in cancer and involve various folate-dependent enzymes. Antifolates have a proven record as clinically used oncolytic agents. Our recent research efforts have produced LSN 3213128 (compound 28a), a novel, selective, nonclassical, orally bioavailable antifolate with potent and specific inhibitory activity for aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFT), an enzyme in the purine biosynthetic pathway. Inhibition of AICARFT with compound 28a results in dramatic elevation of 5-aminoimidazole 4-carboxamide ribonucleotide (ZMP) and growth inhibition in NCI-H460 and MDA-MB-231met2 cancer cell lines. Treatment with this inhibitor in a murine based xenograft model of triple negative breast cancer (TNBC) resulted in tumor growth inhibition.

Organizational Affiliation

Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States.

Macromolecule Content

Total Structure Weight: 267.49 kDa
Atom Count: 18,442
Modelled Residue Count: 2,356
Deposited Residue Count: 2,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional purine biosynthesis protein PURH	A, B, C, D	601	Homo sapiens	Mutation(s): 0 Gene Names: ATIC, PURH, OK/SW-cl.86 EC: 2.1.2.3 (PDB Primary Data), 3.5.4.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P31939 (Homo sapiens) Explore P31939 Go to UniProtKB: P31939
PHAROS: P31939 GTEx: ENSG00000138363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31939
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8UM Query on 8UM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], L [auth C], P [auth D]	5-[(5S)-5-ethyl-5-methyl-6-oxo-1,4,5,6-tetrahydropyridin-3-yl]-N-(6-fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)thiophene-2-sulfonamide C₂₁ H₂₀ F N₃ O₄ S₂ SNANFQWFSNYTEC-NRFANRHFSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
AMZ Query on AMZ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	F [auth A] G [auth A] J [auth B] M [auth C] N [auth C] F [auth A], G [auth A], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE C₉ H₁₅ N₄ O₈ P NOTGFIUVDGNKRI-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	H [auth A], K [auth B], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]