9F1A | pdb_00009f1a

Crystal structure of human soluble epoxide hydrolase C-terminal domain in complex with a benzohomoadamantane-based urea inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9F1A/pdb

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


• Deposited: 2024-04-18 Released: 2025-04-30 
• Deposition Author(s): Qiu, Q., Prischi, F., Jora, B., Vazquez, S., Conte, M.R.
• Funding Organization(s): King's College London

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human soluble epoxide hydrolase C-terminal domain in complex with UB-BJ-05 (20)

Qiu, Q., Prischi, F., Conte, M.R., Jora, B., Vazquez, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 80.14 kDa 
• Atom Count: 5,282 
• Modeled Residue Count: 632 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A, B	344	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H8Y (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-(2,3-dimethoxy-9-methyl-5,6,8,9,10,11-hexahydro-7H-5,9:7,11-dimethanobenzo[9]annulen-7-yl)-3-(1-(tetrahydro-2H-pyran-4-carbonyl)piperidin-4-yl)urea C30 H43 N3 O5 VLPVTKWHYLFBTG-AMIQKGEKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.019	α = 90
b = 81.756	β = 90.54
c = 108.112	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Qiu, Q., Prischi, F., Jora, B., Vazquez, S., Conte, M.R.

---

Funding Organization	Location	Grant Number
King's College London	United Kingdom	--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release