3K4F

X-Ray Crystal Structure of Human Heme Oxygenase-1 in Complex with 4-Phenyl-1-(1H-1,2,4-triazol-1-yl)-2-butanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Heme Oxygenase Inhibition by 2-Oxy-substituted 1-Azolyl-4-phenylbutanes: Effect of Variation of the Azole Moiety. X-Ray Crystal Structure of Human Heme Oxygenase-1 in Complex with 4-Phenyl-1-(1H-1,2,4-triazol-1-yl)-2-butanone.

Roman, G.Rahman, M.N.Vukomanovic, D.Jia, Z.Nakatsu, K.Szarek, W.A.

(2010) Chem Biol Drug Des 75: 68-90

  • DOI: 10.1111/j.1747-0285.2009.00909.x
  • Primary Citation of Related Structures:  
    3K4F

  • PubMed Abstract: 
  • A series of 1-azolyl-4-phenyl-2-butanones was designed and synthesized for the inhibition of heme oxygenases (heme oxygenase-1 and heme oxygenase-2). The replacement of imidazole by other azoles led to the discovery of novel 1H-1,2,4-triazole- and 1H-tetrazole-based inhibitors equipotent to a lead imidazole-based inhibitor ...

    A series of 1-azolyl-4-phenyl-2-butanones was designed and synthesized for the inhibition of heme oxygenases (heme oxygenase-1 and heme oxygenase-2). The replacement of imidazole by other azoles led to the discovery of novel 1H-1,2,4-triazole- and 1H-tetrazole-based inhibitors equipotent to a lead imidazole-based inhibitor. The inhibitors featuring 2H-tetrazole or 1H-1,2,3-triazole as the pharmacophore were less potent. Monosubstitution at position 2 or 4(5), or identical disubstitution at positions 4 and 5 of imidazole by a variety of electron-withdrawing or electron-donating, small or bulky groups, as well as the replacement of the traditional imidazole pharmacophore by an array of 3- or 5-substituted triazoles, identically 3,5-disubstituted triazoles, 5-substituted-1H- and 5-substituted-2H-tetrazoles proved to be detrimental to the inhibition of HO, with a few exceptions. The azole-dioxolanes and the azole-alcohols derived from the active azole-ketones were synthesized also, but these inhibitors were less active than the corresponding imidazole-based analogs. The first reported X-ray crystal structure of human heme oxygenase-1 in complex with a 1,2,4-triazole-based inhibitor, namely 4-phenyl-1-(1H-1,2,4-triazol-1-yl)-2-butanone, was also determined. The inhibitor binds to the human heme oxygenase-1 distal pocket through the coordination of heme iron by the N4 in the triazole moiety, whereas the phenyl group is stabilized by hydrophobic interactions from residues within the binding pocket.


    Organizational Affiliation

    Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme oxygenase 1A, B233Homo sapiensMutation(s): 0 
Gene Names: HMOX1HOHO1
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
Find proteins for P09601 (Homo sapiens)
Explore P09601 
Go to UniProtKB:  P09601
NIH Common Fund Data Resources
PHAROS:  P09601
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Q86
Query on Q86

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]4-phenyl-1-(1H-1,2,4-triazol-1-yl)butan-2-one
C12 H13 N3 O
WVMHBWUDAPTOQF-UHFFFAOYSA-N
 Ligand Interaction
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], J [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.205α = 90
b = 52.483β = 90.21
c = 73.977γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-10-05 
  • Released Date: 2009-12-15 
  • Deposition Author(s): Rahman, M.N., Jia, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance