4HAI

Crystal structure of human soluble epoxide hydrolase complexed with N-cycloheptyl-1-(mesitylsulfonyl)piperidine-4-carboxamide.

• PDB DOI: https://doi.org/10.2210/pdb4HAI/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-09-26 Released: 2012-12-26 
• Deposition Author(s): Pecic, S., Pakhomova, S., Newcomer, M.E., Morisseau, C., Hammock, B.D., Zhu, Z., Deng, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.236 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Synthesis and structure-activity relationship of piperidine-derived non-urea soluble epoxide hydrolase inhibitors.

Pecic, S., Pakhomova, S., Newcomer, M.E., Morisseau, C., Hammock, B.D., Zhu, Z., Rinderspacher, A., Deng, S.X.

(2013) Bioorg Med Chem Lett 23: 417-421

• PubMed: 23237835 
• DOI: https://doi.org/10.1016/j.bmcl.2012.11.084
• Primary Citation of Related Structures:  
  4HAI


• PubMed Abstract: 
  

  A series of potent amide non-urea inhibitors of soluble epoxide hydrolase (sEH) is disclosed. The inhibition of soluble epoxide hydrolase leads to elevated levels of epoxyeicosatrienoic acids (EETs), and thus inhibitors of sEH represent one of a novel approach to the development of vasodilatory and anti-inflammatory drugs. Structure-activities studies guided optimization of a lead compound, identified through high-throughput screening, gave rise to sub-nanomolar inhibitors of human sEH with stability in human liver microsomal assay suitable for preclinical development.

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Organizational Affiliation: 

Department of Medicine, Columbia University, 650 W 168th Street, BB1029, New York, NY 10032, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.21 kDa 
• Atom Count: 4,389 
• Modelled Residue Count: 548 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 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 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I23	D [auth A]	N-cycloheptyl-1-[(2,4,6-trimethylphenyl)sulfonyl]piperidine-4-carboxamide C22 H34 N2 O3 S GTZJATJFRQCZIY-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I23	PDBBind:  4HAI	IC50: 7.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.236 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.32	α = 90
b = 92.32	β = 90
c = 243.982	γ = 120

Software Package:

Software Name	Purpose
xia2	data scaling
MOLREP	phasing
REFMAC	refinement
xia2	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Pecic, S., Pakhomova, S., Newcomer, M.E., Morisseau, C., Hammock, B.D., Zhu, Z., Deng, S.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description