3PDC Hydrolase Hydrolase Inhibitor date Oct 22, 2010
title Crystal Structure Of Hydrolase Domain Of Human Soluble Epoxi Hydrolase Complexed With A Benzoxazole Inhibitor
authors R.G.Kurumbail, J.M.Williams
compound source
Molecule: Epoxide Hydrolase 2
Chain: A, B
Fragment: Hydrolase Domain (Unp Residues 226 To 548)
Synonym: Cytosolic Epoxide Hydrolase, Ceh, Epoxide Hydratas Epoxide Hydrolase, Seh;
Ec: 3.3.2.10
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ephx2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf21
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.279 R_Free 0.333
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.523 79.902 89.318 90.00 90.22 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand ZYI enzyme Hydrolase E.C.3.3.2.10 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiscovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening., Xing L, McDonald JJ, Kolodziej SA, Kurumbail RG, Williams JM, Warren CJ, O'Neal JM, Skepner JE, Roberds SL, J Med Chem. 2011 Mar 10;54(5):1211-22. Epub 2011 Feb 8. PMID:21302953
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdc.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 3PDC
  • CSU: Contacts of Structural Units for 3PDC
  • Structure Factors (284 Kb)
  • Retrieve 3PDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDC from S2C, [Save to disk]
  • Re-refined 3pdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDC in 3D
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  • Visual 3D analysis of 3PDC
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3PDC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdc] [3pdc_B] [3pdc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3PDC
  • Community annotation for 3PDC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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