4EYW

Crystal structure of rat carnitine palmitoyltransferase 2 in complex with 1-[(R)-2-(3,4-Dihydro-1H-isoquinoline-2-carbonyl)-piperidin-1-yl]-2-phenoxy-ethanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.885 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein.

Perspicace, S.Rufer, A.C.Thoma, R.Mueller, F.Hennig, M.Ceccarelli, S.Schulz-Gasch, T.Seelig, J.

(2013) FEBS Open Bio 3: 204-211

  • DOI: 10.1016/j.fob.2013.04.003
  • Primary Citation of Related Structures:  4EP9, 4EPH

  • PubMed Abstract: 
  • Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated ...

    Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of K D = 2-20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery.


    Organizational Affiliation

    Division of Biophysical Chemistry, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carnitine O-palmitoyltransferase 2, mitochondrial
A, B
634Rattus norvegicusGene Names: Cpt2 (Cpt-2)
EC: 2.3.1.21
Find proteins for P18886 (Rattus norvegicus)
Go to UniProtKB:  P18886
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download SDF File 
Download CCD File 
A, B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
L0R
Query on L0R

Download SDF File 
Download CCD File 
A, B
1-[(2R)-2-(3,4-dihydroisoquinolin-2(1H)-ylcarbonyl)piperidin-1-yl]-2-phenoxyethanone
C23 H26 N2 O3
CJQMUNJPWNNVDR-OAQYLSRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.885 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 148.144α = 90.00
b = 148.144β = 90.00
c = 192.070γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description