3OTQ

Soluble Epoxide Hydrolase in complex with pyrazole antagonist

• PDB DOI: https://doi.org/10.2210/pdb3OTQ/pdb

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


• Deposited: 2010-09-13 Released: 2010-10-27 
• Deposition Author(s): Farrow, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.230 

Literature

Substituted pyrazoles as novel sEH antagonist: investigation of key binding interactions within the catalytic domain.

Lo, H.Y., Man, C.C., Fleck, R.W., Farrow, N.A., Ingraham, R.H., Kukulka, A., Proudfoot, J.R., Betageri, R., Kirrane, T., Patel, U., Sharma, R., Hoermann, M.A., Kabcenell, A., Lombaert, S.D.

(2010) Bioorg Med Chem Lett 20: 6379-6383

• PubMed: 20934334 
• DOI: https://doi.org/10.1016/j.bmcl.2010.09.095
• Primary Citation of Related Structures:  
  3OTQ


• PubMed Abstract: 
  

  A novel series of pyrazole sEH inhibitors is reported. Lead optimization efforts to replace the aniline core are also described. In particular, 2-pyridine, 3-pyridine and pyridazine analogs are potent sEH inhibitors with favorable CYP3A4 inhibitory and microsomal stability profiles.

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Organizational Affiliation: 

Boehringer Ingelheim Pharmaceuticals Inc., Biomolecular Screening, 900 Ridgebury Rd., PO Box 368, Ridgefield, CT 06877, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.06 kDa 
• Atom Count: 4,385 
• Modelled Residue Count: 545 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase 2	A	555	Homo sapiens	Mutation(s): 0  Gene Names: EPHX2 EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens) Explore P34913  Go to UniProtKB:  P34913
PHAROS:  P34913 GTEx:  ENSG00000120915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MZL	B [auth A]	N-[4-(5-ethyl-3-pyridin-3-yl-1H-pyrazol-1-yl)phenyl]pyridine-3-carboxamide C22 H19 N5 O CCAFHMPMIJBDRP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MZL	BindingDB:  3OTQ	IC50: 41 (nM) from 1 assay(s)
	PDBBind:  3OTQ	IC50: 41 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.230 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.993	α = 90
b = 92.993	β = 90
c = 243.651	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Farrow, N.A.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-24
  Changes: Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references