7OXL

Crystal structure of human Spermine Oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 1.5.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWM0 (Homo sapiens)
Explore Q9NWM0 
Go to UniProtKB:  Q9NWM0
PHAROS:  Q9NWM0
GTEx:  ENSG00000088826 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWM0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.919α = 90
b = 190.919β = 90
c = 43.574γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6YUClick on this verticalbar to view details

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
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary