9JFM | pdb_00009jfm

Co-crystal Structure of sEH with tetrahydroberberine derivative

• PDB DOI: https://doi.org/10.2210/pdb9JFM/pdb

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


• Deposited: 2024-09-04 Released: 2025-09-10 
• Deposition Author(s): Wang, H., Feng, Y., Du, X.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Co-crystal Structure of sEH with tetrahydroberberine derivative

Wang, H., Feng, Y., Du, X.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.33 kDa 
• Atom Count: 4,383 
• Modeled 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
A1EBK (Subject of Investigation/LOI)	D [auth A]	1-[(13~{a}~{R})-2,3-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[3,2-a]isoquinolin-10-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea C28 H28 F3 N3 O4 QLVMEJODLSQJTN-XMMPIXPASA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.89	α = 90
b = 91.89	β = 90
c = 244.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Wang, H., Feng, Y., Du, X.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release