Crystal structure of rat carnitine palmitoyltransferase 2 in complex with r-3-(hexadecanoylamino)-4-(trimethylazaniumyl)butanoate

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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This is version 1.6 of the entry. See complete history


Carnitine palmitoyltransferase 2: analysis of membrane association and complex structure with a substrate analog.

Rufer, A.C.Lomize, A.Benz, J.Chomienne, O.Thoma, R.Hennig, M.

(2007) FEBS Lett 581: 3247-3252

  • DOI: https://doi.org/10.1016/j.febslet.2007.05.080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The mitochondrial membrane-associated carnitine palmitoyltransferase system is a validated target for the treatment of type 2 diabetes mellitus. To further facilitate structure-based drug discovery, we determined the crystal structure of rat CPT-2 (rCPT-2) in complex with the substrate analogue palmitoyl-aminocarnitine at 1.8A resolution. Biochemical analyses revealed a strong effect of this compound on rCPT-2 activity and stability. Using a computational approach we examined the membrane association of rCPT-2. The protein interacts with the membrane as a functional monomer and the calculations confirm the presence of a membrane association domain that consists of layers of hydrophobic and positively charged residues.

  • Organizational Affiliation

    F Hoffmann-La Roche AG, Pharma Research Discovery, Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carnitine O-palmitoyltransferase 2
A, B
653Rattus norvegicusMutation(s): 0 
Gene Names: Cpt2Cpt-2
Find proteins for P18886 (Rattus norvegicus)
Explore P18886 
Go to UniProtKB:  P18886
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18886
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BUJ

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
C23 H46 N2 O3
Query on BOG

Download Ideal Coordinates CCD File 
C [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
BUJ Binding MOAD:  2RCU IC50: 210 (nM) from 1 assay(s)
PDBBind:  2RCU IC50: 210 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.273α = 90
b = 97.75β = 90
c = 312.05γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-09-25
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2021-05-05
    Changes: Data collection, Structure summary
  • Version 1.6: 2023-08-30
    Changes: Data collection, Database references, Refinement description