1MX9

Crystal Structure of Human Liver Carboxylesterase in complexed with naloxone methiodide, a heroin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis of Heroin and Cocaine Metabolism by a Promiscuous Human Drug-Processing Enzyme

Bencharit, S.Morton, C.L.Xue, Y.Potter, P.M.Redinbo, M.R.

(2003) Nat Struct Biol 10: 349-356

  • DOI: https://doi.org/10.1038/nsb919
  • Primary Citation of Related Structures:  
    1MX5, 1MX9

  • PubMed Abstract: 

    We present the first crystal structures of a human protein bound to analogs of cocaine and heroin. Human carboxylesterase 1 (hCE1) is a broad-spectrum bioscavenger that catalyzes the hydrolysis of heroin and cocaine, and the detoxification of organophosphate chemical weapons, such as sarin, soman and tabun. Crystal structures of the hCE1 glycoprotein in complex with the cocaine analog homatropine and the heroin analog naloxone provide explicit details about narcotic metabolism in humans. The hCE1 active site contains both specific and promiscuous compartments, which enable the enzyme to act on structurally distinct chemicals. A selective surface ligand-binding site regulates the trimer-hexamer equilibrium of hCE1 and allows each hCE1 monomer to bind two narcotic molecules simultaneously. The bioscavenger properties of hCE1 can likely be used to treat both narcotic overdose and chemical weapon exposure.


  • Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
liver Carboxylesterase I
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NLX
Query on NLX

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
EA [auth I]
GA [auth J]
IA [auth K]
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
IA [auth K],
KA [auth L],
O [auth A],
Q [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
(5A,17R)-4,5-EPOXY-3,14-DIHYDROXY-17-METHYL-6-OXO-17-(2-PROPENYL)-MORPHINANIUM
C20 H24 N O4
PCSQOABIHJXZMR-YNUHATHGSA-O
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
M [auth A],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.174α = 90.28
b = 120.711β = 89.32
c = 177.017γ = 99.22
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    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 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary