1HU9

LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of curcumin in complex with lipoxygenase and its significance in cancer.

Skrzypczak-Jankun, E.Zhou, K.McCabe, N.P.Selman, S.H.Jankun, J.

(2003) Int J Mol Med 12: 17-24

  • Primary Citation of Related Structures:  
    1HU9

  • PubMed Abstract: 
  • Scientific research provides documented evidence that fatty acid metabolites have profound impact on carcinogenesis. Intervention into dioxygenase pathways might therefore effect development, metastasis and progression of many types of cancers. This work delivers the first 3D structural data and explains how curcumin interacts with the fatty acid metabolizing enzyme, soybean lipoxygenase ...

    Scientific research provides documented evidence that fatty acid metabolites have profound impact on carcinogenesis. Intervention into dioxygenase pathways might therefore effect development, metastasis and progression of many types of cancers. This work delivers the first 3D structural data and explains how curcumin interacts with the fatty acid metabolizing enzyme, soybean lipoxygenase. Curcumin binds to lipoxygenase in a non-competitive manner. Trapped in that complex, it undergoes photodegradation in the X-rays, but utilizes enzyme catalytic ability to form the peroxy complex Enz-Fe-O-O-R as 4-hydroperoxy-2-methoxy-phenol, that later transforms into 2-methoxycyclohexa-2,5-diene-1,4-dione. Our observations about this radiation and time-dependent inhibition add new information to the role that curcumin might play in cancer prevention and treatment.


    Related Citations: 
    • Curcumin Inhibits Lipooxygenase by Binding to its Center Cavity: Theoretical and X-Ray Evidence
      Skrzypczak-Jankun, E., McCabe, N.P., Selman, S.H., Jankun, J.
      (2000) Int J Mol Med 6: 521
    • Structure of Soybean Lipoxygenase L3 and a Comparison with its L1 Isoenzyme
      Skrzypczak-Jankun, E., Amzel, L.M., Kroa, B.A., Funk Jr., M.O.
      (1997) Proteins 29: 15
    • Structural and Thermochemical Characterization of Lipoxygenase-Catechol Complexes
      Pham, C., Jankun, J., Skrzypczak-Jankun, E., Flowers II, R.A., Funk Jr., M.O.
      (1998) Biochemistry 37: 17952
    • Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3
      Kramer, J.A., Johnson, K.R., Dunham, W.R., Sands, R.H., Funk Jr., M.O.
      (1994) Biochemistry 33: 15017

    Organizational Affiliation

    Department of Urology, Urology Research Center, Medical College of Ohio, Toledo, OH 43614-5807, USA. ewa@golemxiv.dk.mco.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIPOXYGENASE-3A857Glycine maxMutation(s): 0 
Gene Names: LOX1.3LOX3
EC: 1.13.11.12 (PDB Primary Data), 1.13.11.58 (UniProt)
UniProt
Find proteins for P09186 (Glycine max)
Explore P09186 
Go to UniProtKB:  P09186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09186
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4HM
Query on 4HM

Download Ideal Coordinates CCD File 
C [auth A]4-HYDROPEROXY-2-METHOXY-PHENOL
C7 H8 O4
DNBCLSZROQUYQN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.79α = 90
b = 137.32β = 95.55
c = 61.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection