3K4F | pdb_00003k4f

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 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1111/j.1747-0285.2009.00909.x
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 55.89 kDa 
  • Atom Count: 3,905 
  • Modeled Residue Count: 428 
  • Deposited Residue Count: 466 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heme oxygenase 1
A, B
233Homo sapiensMutation(s): 0 
Gene Names: HMOX1HOHO1
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09601 (Homo sapiens)
Explore P09601 
Go to UniProtKB:  P09601
PHAROS:  P09601
GTEx:  ENSG00000100292 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09601
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
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
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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description