1MX1 | pdb_00001mx1

Crystal Structure of Human Liver Carboxylesterase in complex with tacrine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.207 (Depositor) 
  • R-Value Work: 
    0.162 (Depositor) 
  • R-Value Observed: 
    0.162 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1MX1

This is version 3.0 of the entry. See complete history

Literature

Crystal Structure of Human Carboxylesterase 1 Complexed with the Alzheimer's Drug Tacrine: From Binding Promiscuity to Selective Inhibition

Bencharit, S.Morton, C.L.Hyatt, J.L.Kuhn, P.Danks, M.K.Potter, P.M.Redinbo, M.R.

(2003) Chem Biol 10: 341-349

  • DOI: https://doi.org/10.1016/s1074-5521(03)00071-1
  • Primary Citation Related Structures: 
    1MX1

  • PubMed Abstract: 

    Human carboxylesterase 1 (hCE1) is a broad-spectrum bioscavenger that plays important roles in narcotic metabolism, clinical prodrug activation, and the processing of fatty acid and cholesterol derivatives. We determined the 2.4 A crystal structure of hCE1 in complex with tacrine, the first drug approved for treating Alzheimer's disease, and compare this structure to the Torpedo californica acetylcholinesterase (AcChE)-tacrine complex. Tacrine binds in multiple orientations within the catalytic gorge of hCE1, while it stacks in the smaller AcChE active site between aromatic side chains. Our results show that hCE1's promiscuous action on distinct substrates is enhanced by its ability to interact with ligands in multiple orientations at once. Further, we use our structure to identify tacrine derivatives that act as low-micromolar inhibitors of hCE1 and may provide new avenues for treating narcotic abuse and cholesterol-related diseases.


  • Organizational Affiliation
    • Department of Chemistry, School of Dentistry, University of North Carolina, Chapel Hill, 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 367.25 kDa 
  • Atom Count: 27,468 
  • Modeled Residue Count: 3,187 
  • Deposited Residue Count: 3,288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
liver Carboxylesterase I
A, B, C, D, E
A, B, C, D, E, F
548Homo 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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G07375KG
GlyCosmos: G07375KG
GlyGen: G07375KG

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA

Query on SIA



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

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A]
K [auth B]
O [auth D]
R [auth E]
U [auth F]
H [auth A],
K [auth B],
O [auth D],
R [auth E],
U [auth F],
V [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
THA

Query on THA



Download:Ideal Coordinates CCD File
J [auth A]
M [auth B]
N [auth C]
Q [auth D]
T [auth E]
J [auth A],
M [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
TACRINE
C13 H14 N2
YLJREFDVOIBQDA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
THA BindingDB:  1MX1 Ki: 1.00e+5 (nM) from 1 assay(s)
IC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.207 (Depositor) 
  • R-Value Work:  0.162 (Depositor) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.021α = 90
b = 117.03β = 95.69
c = 176.01γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary