5NHY | pdb_00005nhy

BAY-707 in complex with MTH1

• PDB DOI: https://doi.org/10.2210/pdb5NHY/pdb

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


• Deposited: 2017-03-22 Released: 2017-07-19 
• Deposition Author(s): Ellermann, M., Eheim, A., Giese, A., Bunse, S., Nowak-Reppel, K., Neuhaus, R., Weiske, J., Quanz, M., Glasauer, A., Meyer, H., Queisser, N., Irlbacher, H., Bader, B., Rahm, F., Viklund, J., Andersson, M., Ericsson, U., Ginman, T., Forsblom, R., Lindstrom, J., Silvander, C., Tresaugues, L., Gorjanacz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Novel Class of Potent and Cellularly Active Inhibitors Devalidates MTH1 as Broad-Spectrum Cancer Target.

Ellermann, M., Eheim, A., Rahm, F., Viklund, J., Guenther, J., Andersson, M., Ericsson, U., Forsblom, R., Ginman, T., Lindstrom, J., Silvander, C., Tresaugues, L., Giese, A., Bunse, S., Neuhaus, R., Weiske, J., Quanz, M., Glasauer, A., Nowak-Reppel, K., Bader, B., Irlbacher, H., Meyer, H., Queisser, N., Bauser, M., Haegebarth, A., Gorjanacz, M.

(2017) ACS Chem Biol 12: 1986-1992

• PubMed: 28679043 
• DOI: https://doi.org/10.1021/acschembio.7b00370
• Primary Citation Related Structures: 
  5NHY


• PubMed Abstract: 
  

  MTH1 is a hydrolase responsible for sanitization of oxidized purine nucleoside triphosphates to prevent their incorporation into replicating DNA. Early tool compounds published in the literature inhibited the enzymatic activity of MTH1 and subsequently induced cancer cell death; however recent studies have questioned the reported link between these two events. Therefore, it is important to validate MTH1 as a cancer dependency with high quality chemical probes. Here, we present BAY-707, a substrate-competitive, highly potent and selective inhibitor of MTH1, chemically distinct compared to those previously published. Despite superior cellular target engagement and pharmacokinetic properties, inhibition of MTH1 with BAY-707 resulted in a clear lack of in vitro or in vivo anticancer efficacy either in mono- or in combination therapies. Therefore, we conclude that MTH1 is dispensable for cancer cell survival.

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Organizational Affiliation: 
• Bayer AG , Berlin, Germany.
Sprint Bioscience , Huddinge, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.03 kDa 
• Atom Count: 2,763 
• Modeled Residue Count: 306 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine triphosphatase	A, B	159	Homo sapiens	Mutation(s): 0  Gene Names: NUDT1, MTH1 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639  Go to UniProtKB:  P36639
PHAROS:  P36639 GTEx:  ENSG00000106268

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8XT	C [auth A], K [auth B]	~{N}-ethyl-4-[(3~{S})-3-methylmorpholin-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine-2-carboxamide C15 H20 N4 O2 RPMGXDCRCWWCRY-JTQLQIEISA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8XT	BindingDB:  5NHY	IC50: min: 0.8, max: 2.3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.528	α = 90
b = 66.709	β = 90
c = 82.075	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Ellermann, M., Eheim, A., Giese, A., Bunse, S., Nowak-Reppel, K., Neuhaus, R., Weiske, J., Quanz, M., Glasauer, A., Meyer, H., Queisser, N., Irlbacher, H., Bader, B., Rahm, F., Viklund, J., Andersson, M., Ericsson, U., Ginman, T., Forsblom, R., Lindstrom, J., Silvander, C., Tresaugues, L., Gorjanacz, M.

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description