4C4Y | pdb_00004c4y

Crystal structure of human bifunctional epoxide hydroxylase 2 complexed with A4

• PDB DOI: https://doi.org/10.2210/pdb4C4Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-09 Released: 2014-10-01 
• Deposition Author(s): Pilger, J., Mazur, A., Monecke, P., Schreuder, H., Elshorst, B., Langer, T., Schiffer, A., Krimm, I., Wegstroth, M., Lee, D., Hessler, G., Wendt, K.-U., Becker, S., Griesinger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.315 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles.

Pilger, J., Mazur, A., Monecke, P., Schreuder, H., Elshorst, B., Bartoschek, S., Langer, T., Schiffer, A., Krimm, I., Wegstroth, M., Lee, D., Hessler, G., Wendt, K., Becker, S., Griesinger, C.

(2015) Angew Chem Int Ed Engl 54: 6511

• PubMed: 25877959 
• DOI: https://doi.org/10.1002/anie.201500671
• Primary Citation Related Structures: 
  4C4X, 4C4Y, 4C4Z, 4YXR, 4YXS


• PubMed Abstract: 
  

  Structure-based drug design (SBDD) is a powerful and widely used approach to optimize affinity of drug candidates. With the recently introduced INPHARMA method, the binding mode of small molecules to their protein target can be characterized even if no spectroscopic information about the protein is known. Here, we show that the combination of the spin-diffusion-based NMR methods INPHARMA, trNOE, and STD results in an accurate scoring function for docking modes and therefore determination of protein-ligand complex structures. Applications are shown on the model system protein kinase A and the drug targets glycogen phosphorylase and soluble epoxide hydrolase (sEH). Multiplexing of several ligands improves the reliability of the scoring function further. The new score allows in the case of sEH detecting two binding modes of the ligand in its binding site, which was corroborated by X-ray analysis.

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Organizational Affiliation: 
• Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Germany).
Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt a. M. (Germany).
Université Claude Bernard Lyon1, Villeurbanne Cedex (France).
Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Germany). [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.6 kDa 
• Atom Count: 2,689 
• Modeled Residue Count: 314 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL EPOXIDE HYDROLASE 2	A	326	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7WI	B [auth A]	1-(3-chlorophenyl)-3-(2-methoxyethyl)urea C10 H13 Cl N2 O2 OCWOGWHGSTYVMJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.315 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.64	α = 90
b = 46.34	β = 90
c = 80.29	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Pilger, J., Mazur, A., Monecke, P., Schreuder, H., Elshorst, B., Langer, T., Schiffer, A., Krimm, I., Wegstroth, M., Lee, D., Hessler, G., Wendt, K.-U., Becker, S., Griesinger, C.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references
• Version 1.2: 2015-06-10
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.5: 2021-02-24
  Changes: Derived calculations, Other
• Version 1.6: 2021-03-31
  Changes: Derived calculations
• Version 1.7: 2023-12-20
  Changes: Data collection, Database references, Refinement description