6N3K

Crystal structure of an epoxide hydrolase from Trichoderma reesei in complex with inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The molecular structure of an epoxide hydrolase from Trichoderma reesei in complex with urea or amide-based inhibitors.

de Oliveira, G.S.Adriani, P.P.Ribeiro, J.A.Morisseau, C.Hammock, B.D.Dias, M.V.B.Chambergo, F.S.

(2019) Int J Biol Macromol 129: 653-658

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.02.070
  • Primary Citation of Related Structures:  
    6N3K, 6N3Z, 6N5F, 6N5G, 6N5H

  • PubMed Abstract: 

    Epoxide hydrolases (EHs) are enzymes involved in the metabolism of endogenous and exogenous epoxides, and the development of EH inhibitors has important applications in the medicine. In humans, EH inhibitors are being tested in the treatment of cardiovascular diseases and show potent anti-inflammatory effects. EH inhibitors are also considerate promising molecules against infectious diseases. EHs are functionally very well studied, but only a few members have its three-dimensional structures characterized. Recently, a new EH from the filamentous fungi Trichoderma reseei (TrEH) was reported, and a series of urea or amide-based inhibitors were identified. In this study, we describe the crystallographic structures of TrEH in complex with five different urea or amide-based inhibitors with resolutions ranging from 2.6 to 1.7 Å. The analysis of these structures reveals the molecular basis of the inhibition of these compounds. We could also observe that these inhibitors occupy the whole extension of the active site groove and only a few conformational changes are involved. Understanding the structural basis EH interactions with different inhibitors might substantially contribute for the study of fungal metabolism and in the development of novel and more efficient antifungal drugs against pathogenic Trichoderma species.


  • Organizational Affiliation

    Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, 1000 Arlindo Bettio Avenue, 03828-000 São Paulo, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epoxide hydrolase336Trichoderma reesei QM9414Mutation(s): 0 
Gene Names: TrEH
UniProt
Find proteins for G0R7E2 (Hypocrea jecorina (strain QM6a))
Explore G0R7E2 
Go to UniProtKB:  G0R7E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0R7E2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K9V
Query on K9V

Download Ideal Coordinates CCD File 
B [auth A]N-{cis-4-[(2,6-difluorophenyl)methoxy]cyclohexyl}-N'-(3-phenylpropyl)urea
C23 H28 F2 N2 O2
YXIUOVJEXYHABJ-KDURUIRLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.073α = 90
b = 77.276β = 90
c = 87.103γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2015/03329
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesNIEHS-R01 ES002710
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesP42 ES 04699
Sao Paulo Research Foundation (FAPESP)Brazil2014/24107-1
Sao Paulo Research Foundation (FAPESP)Brazil2017/25705-8
Sao Paulo Research Foundation (FAPESP)Brazil2015/09188-8
Sao Paulo Research Foundation (FAPESP)Brazil2018/00351-1
Sao Paulo Research Foundation (FAPESP)Brazil2016/12859-4
Sao Paulo Research Foundation (FAPESP)Brazil2013/15906-5
Fundacao para a Ciencia e a TecnologiaBrazil142311/2016-2

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description