1YA8

Crystal Structure of Human Liver Carboxylesterase in complex with cleavage products of Mevastatin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 Biol 352: 165-177

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CES1 protein A, B, C532Homo sapiensMutation(s): 0 
Gene Names: CES1, CES2, SES1
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.13 (UniProt), 3.1.1.56 (UniProt)
Find proteins for P23141 (Homo sapiens)
Explore P23141 
Go to UniProtKB:  P23141
NIH Common Fund Data Resources
PHAROS:  P23141
GTEx:  ENSG00000198848
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA
Download Ideal Coordinates CCD File 
A, B, C
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N		 Ligand Interaction
MVB
Query on MVB
Download Ideal Coordinates CCD File 
A, C
(1S,7S,8S,8AR)-1,2,3,7,8,8A-HEXAHYDRO-7-METHYL-8-[2-[(2R,4R)-TETRAHYDRO-4-HY DROXY-6-OXO-2H-PYRAN-2-YL]ETHYL]-1-NAPHTHALENOL
C18 H26 O4
WWSNTLOVYSRDEL-TVKPWXLESA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SMB
Query on SMB
Download Ideal Coordinates CCD File 
A, B, C
2-METHYLBUTANOIC ACID
C5 H10 O2
WLAMNBDJUVNPJU-BYPYZUCNSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.777α = 90
b = 181.589β = 90
c = 202.874γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
CCP4data scaling
AMoREphasing

Structure Validation

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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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary