9KWL | pdb_00009kwl

hCES1A contently binding with compound F-3 at the catalytic pocket.

• PDB DOI: https://doi.org/10.2210/pdb9KWL/pdb

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


• Deposited: 2024-12-06 Released: 2025-01-29 
• Deposition Author(s): Gai, C., Zhao, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The study of halogen effect on the reactivity of the serine-targeting covalent warheads.

Gai, C., Zhang, Y., Zhang, S., Hu, X., Song, Y.Q., Zhuang, X., Chai, X., Zou, Y., Ge, G.B., Zhao, Q.

(2024) Front Chem 12: 1504453-1504453

• PubMed: 39691824 
• DOI: https://doi.org/10.3389/fchem.2024.1504453
• Primary Citation Related Structures: 
  9KWL, 9KWM


• PubMed Abstract: 
  

  Halogens favorably contributes to the drug potency and metabolic stability via electrostatic interactions. Herein, the halogen effects on the reactivity of the halogenated 2,2,2-trifluoroacetophenones as serine-targeting covalent warheads were investigated. Our results showed that introducing halogen atoms, especially Cl or Br, into the phenyl scaffold would influence the electron density around the ring, which led to different time-dependent inhibition response to the target serine hydrolase (hCES1A). Co-crystallography analysis not only verified that halogenated molecules preferred to form covalent adducts, but also provided the conformational information for the design of covalent inhibitors targeting to hCES1A protein for the treatment of drug-induced acute enteritis.

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Organizational Affiliation: 
• Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China.
Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.07 kDa 
• Atom Count: 4,711 
• Modeled Residue Count: 533 
• Deposited Residue Count: 533 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Liver carboxylesterase 1	A	533	Homo sapiens	Mutation(s): 0  Gene Names: CES1, CES2, SES1 EC: 3.1.1.1 (PDB Primary Data), 3.1.1.13 (PDB Primary Data), 3.1.1.56 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens) Explore P23141  Go to UniProtKB:  P23141
PHAROS:  P23141 GTEx:  ENSG00000198848

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EIY (Subject of Investigation/LOI)	B [auth A]	(1R)-1-(3,4-dichlorophenyl)-2,2,2-tris(fluoranyl)ethanol C8 H5 Cl2 F3 O GOCHXDOXYWWSKG-SSDOTTSWSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.469	α = 90
b = 110.469	β = 90
c = 278.259	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Gai, C., Zhao, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82204347

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release