1YAH | pdb_00001yah

Crystal Structure of Human Liver Carboxylesterase complexed to Etyl Acetate; A Fatty Acid Ethyl Ester Analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.229 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1YAH

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural insights into drug processing by human carboxylesterase 1: tamoxifen, mevastatin, and inhibition by benzil.

Fleming, C.D.Bencharit, S.Edwards, C.C.Hyatt, J.L.Tsurkan, L.Bai, F.Fraga, C.Morton, C.L.Howard-Williams, E.L.Potter, P.M.Redinbo, M.R.

(2005) J Mol Biology 352: 165-177

  • DOI: https://doi.org/10.1016/j.jmb.2005.07.016
  • Primary Citation Related Structures: 
    1YA4, 1YA8, 1YAH, 1YAJ

  • PubMed Abstract: 

    Human carboxylesterase 1 (hCE1) exhibits broad substrate specificity and is involved in xenobiotic processing and endobiotic metabolism. We present and analyze crystal structures of hCE1 in complexes with the cholesterol-lowering drug mevastatin, the breast cancer drug tamoxifen, the fatty acyl ethyl ester (FAEE) analogue ethyl acetate, and the novel hCE1 inhibitor benzil. We find that mevastatin does not appear to be a substrate for hCE1, and instead acts as a partially non-competitive inhibitor of the enzyme. Similarly, we show that tamoxifen is a low micromolar, partially non-competitive inhibitor of hCE1. Further, we describe the structural basis for the inhibition of hCE1 by the nanomolar-affinity dione benzil, which acts by forming both covalent and non-covalent complexes with the enzyme. Our results provide detailed insights into the catalytic and non-catalytic processing of small molecules by hCE1, and suggest that the efficacy of clinical drugs may be modulated by targeted hCE1 inhibitors.


  • Organizational Affiliation
    • Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 178.71 kDa 
  • Atom Count: 12,981 
  • Modeled Residue Count: 1,596 
  • Deposited Residue Count: 1,596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CES1 protein
A, B, C
532Homo sapiensMutation(s): 0 
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.56 (UniProt), 3.1.1.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens)
Explore P23141 
Go to UniProtKB:  P23141
PHAROS:  P23141
GTEx:  ENSG00000198848 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23141
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P23141-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA

Query on SIA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
L [auth B]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B],
P [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
M [auth B]
Q [auth C]
R [auth C]
G [auth A],
H [auth A],
M [auth B],
Q [auth C],
R [auth C],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EEE

Query on EEE



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
N [auth B]
O [auth B]
T [auth C]
I [auth A],
J [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C]
ETHYL ACETATE
C4 H8 O2
XEKOWRVHYACXOJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.229 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.5α = 90
b = 181.15β = 90
c = 203.01γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-09
    Changes: Structure summary