Structure of human Spermine Oxidase in complex with a highly selective allosteric inhibitor

Experimental Data Snapshot

  • Resolution: 2.09 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Structure of human spermine oxidase in complex with a highly selective allosteric inhibitor.

Diaz, E.Adhikary, S.Tepper, A.W.J.W.Riley, D.Ortiz-Meoz, R.Krosky, D.Buyck, C.Lamenca, C.M.Llaveria, J.Fang, L.Kalin, J.H.Klaren, V.N.A.Fahmy, S.Shaffer, P.L.Kirkpatrick, R.Carbajo, R.J.Thomsen, M.Impagliazzo, A.

(2022) Commun Biol 5: 787-787

  • DOI: https://doi.org/10.1038/s42003-022-03735-9
  • Primary Citation of Related Structures:  
    7OXL, 7OY0

  • PubMed Abstract: 

    Human spermine oxidase (hSMOX) plays a central role in polyamine catabolism. Due to its association with several pathological processes, including inflammation and cancer, hSMOX has garnered interest as a possible therapeutic target. Therefore, determination of the structure of hSMOX is an important step to enable drug discovery and validate hSMOX as a drug target. Using insights from hydrogen/deuterium exchange mass spectrometry (HDX-MS), we engineered a hSMOX construct to obtain the first crystal structure of hSMOX bound to the known polyamine oxidase inhibitor MDL72527 at 2.4 Å resolution. While the overall fold of hSMOX is similar to its homolog, murine N1-acetylpolyamine oxidase (mPAOX), the two structures contain significant differences, notably in their substrate-binding domains and active site pockets. Subsequently, we employed a sensitive biochemical assay to conduct a high-throughput screen that identified a potent and selective hSMOX inhibitor, JNJ-1289. The co-crystal structure of hSMOX with JNJ-1289 was determined at 2.1 Å resolution, revealing that JNJ-1289 binds to an allosteric site, providing JNJ-1289 with a high degree of selectivity towards hSMOX. These results provide crucial insights into understanding the substrate specificity and enzymatic mechanism of hSMOX, and for the design of highly selective inhibitors.

  • Organizational Affiliation

    Janssen Research & Development, Welsh & McKean Roads, Spring House, PA, 19477-0776, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermine oxidase,Spermine oxidase,Spermine oxidase494Homo sapiensMutation(s): 0 
Gene Names: SMOXC20orf16SMOUNQ3039/PRO9854
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWM0 (Homo sapiens)
Explore Q9NWM0 
Go to UniProtKB:  Q9NWM0
GTEx:  ENSG00000088826 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWM0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6YU

Download Ideal Coordinates CCD File 
B [auth A]FAD-MDL72527 adduct
C39 H53 N11 O15 P2
Query on 3EI

Download Ideal Coordinates CCD File 
C [auth A]4-[(4-imidazo[1,2-a]pyridin-3-yl-1,3-thiazol-2-yl)amino]phenol
C16 H12 N4 O S
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.09 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.755α = 90
b = 193.755β = 90
c = 44.332γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references