3HOK

X-ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: A Novel, Inducible Binding Mode

• PDB DOI: https://doi.org/10.2210/pdb3HOK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-02 Released: 2009-07-28 
• Deposition Author(s): Rahman, M.N., Jia, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of human heme oxygenase-1 with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane: a novel, inducible binding mode.

Rahman, M.N., Vlahakis, J.Z., Vukomanovic, D., Szarek, W.A., Nakatsu, K., Jia, Z.

(2009) J Med Chem 52: 4946-4950

• PubMed: 19601578 
• DOI: https://doi.org/10.1021/jm900434f
• Primary Citation of Related Structures:  
  3HOK


• PubMed Abstract: 
  

  The crystal structure of human heme oxygenase-1 (HO-1) in complex with (2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4[((5-trifluoromethylpyridin-2-yl)thio)methyl]-1,3-dioxolane (4) reveals a novel, inducible binding mode. Inhibitor 4 coordinates the heme iron, with its chlorophenyl group bound in a distal hydrophobic pocket, as seen in previous structures. However, accommodation of the 5-trifluoromethylpyridin-2-yl group requires a significant shift in the proximal helix, inducing the formation of a hydrophobic pocket. This is the first example of an induced binding pocket observed in HO-1.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.51 kDa 
• Atom Count: 3,802 
• Modelled Residue Count: 429 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase 1	A, B	233	Homo sapiens	Mutation(s): 0  Gene Names: HMOX1, HO, HO1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
Q80	E [auth B]	2-({[(2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methyl}sulfanyl)-5-(trifluoromethyl)pyridine C22 H21 Cl F3 N3 O2 S QJIXKBNNYAEGKH-PZJWPPBQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.072	α = 90
b = 54.592	β = 94.641
c = 71.884	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Rahman, M.N., Jia, Z.

Revision History  

• Version 1.0: 2009-07-28
  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