9GQL | pdb_00009gql

Human MTH1 in complex with stanozolol

• PDB DOI: https://doi.org/10.2210/pdb9GQL/pdb

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


• Deposited: 2024-09-09 Released: 2025-08-13 
• Deposition Author(s): Scaletti Hutchinson, E., Gustafsson Westergren, R., Stenmark, P.
• Funding Organization(s): Cancerfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.153 (DCC) 

Starting Model: experimental

Literature

The anabolic steroid stanozolol is a potent inhibitor of human MutT homolog 1.

Scaletti Hutchinson, E., Gustafsson Westergren, R., Almlof, I., Jemth, A.S., Scobie, M., Warpman Berglund, U., Helleday, T., Stenmark, P.

(2025) FEBS Lett 

• PubMed: 40878820 
• DOI: https://doi.org/10.1002/1873-3468.70116
• Primary Citation of Related Structures:  
  9GQL


• PubMed Abstract: 
  

  Human MutT homolog 1 (hMTH1) removes damaged nucleotides from the nucleotide pool, preventing their incorporation into DNA. Due to its potential as an anticancer drug target, hMTH1 has been the focus of several inhibitor development studies. Unexpectedly, we show that the anabolic steroid stanozolol (Stz) is a potent nanomolar inhibitor of hMTH1. We present the structure of hMTH1 in complex with Stz, which indicates a unique core scaffold that could be exploited for future inhibitor development. Comparison with human protein structures bound with dihydrotestosterone (DHT) shows hMTH1 is entirely unrelated in terms of its structure. As these DHT binding proteins are all involved in steroid regulation, this makes the identification of Stz as a potent hMTH1 inhibitor all the more unusual.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1,456 
• Modeled Residue Count: 154 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized purine nucleoside triphosphate hydrolase	A	156	Homo sapiens	Mutation(s): 0  Gene Names: NUDT1, MTH1 EC: 3.6.1.56 (PDB Primary Data), 3.6.1 (PDB Primary Data)
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
A1IOS (Subject of Investigation/LOI)	B [auth A]	stanozolol C21 H32 N2 O LKAJKIOFIWVMDJ-IYRCEVNGSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.153 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.526	α = 90
b = 59.71	β = 90
c = 66.875	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Scaletti Hutchinson, E., Gustafsson Westergren, R., Stenmark, P.

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Funding Organization	Location	Grant Number
Cancerfonden	Sweden	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references