4F2A

Crystal structure of cholestryl esters transfer protein in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of cholesteryl ester transfer protein in complex with inhibitors.

Liu, S.Mistry, A.Reynolds, J.M.Lloyd, D.B.Griffor, M.C.Perry, D.A.Ruggeri, R.B.Clark, R.W.Qiu, X.

(2012) J.Biol.Chem. 287: 37321-37329

  • DOI: 10.1074/jbc.M112.380063
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human plasma cholesteryl ester transfer protein (CETP) transports cholesteryl ester from the antiatherogenic high-density lipoproteins (HDL) to the proatherogenic low-density and very low-density lipoproteins (LDL and VLDL). Inhibition of CETP has be ...

    Human plasma cholesteryl ester transfer protein (CETP) transports cholesteryl ester from the antiatherogenic high-density lipoproteins (HDL) to the proatherogenic low-density and very low-density lipoproteins (LDL and VLDL). Inhibition of CETP has been shown to raise human plasma HDL cholesterol (HDL-C) levels and is potentially a novel approach for the prevention of cardiovascular diseases. Here, we report the crystal structures of CETP in complex with torcetrapib, a CETP inhibitor that has been tested in phase 3 clinical trials, and compound 2, an analog from a structurally distinct inhibitor series. In both crystal structures, the inhibitors are buried deeply within the protein, shifting the bound cholesteryl ester in the N-terminal pocket of the long hydrophobic tunnel and displacing the phospholipid from that pocket. The lipids in the C-terminal pocket of the hydrophobic tunnel remain unchanged. The inhibitors are positioned near the narrowing neck of the hydrophobic tunnel of CETP and thus block the connection between the N- and C-terminal pockets. These structures illuminate the unusual inhibition mechanism of these compounds and support the tunnel mechanism for neutral lipid transfer by CETP. These highly lipophilic inhibitors bind mainly through extensive hydrophobic interactions with the protein and the shifted cholesteryl ester molecule. However, polar residues, such as Ser-230 and His-232, are also found in the inhibitor binding site. An enhanced understanding of the inhibitor binding site may provide opportunities to design novel CETP inhibitors possessing more drug-like physical properties, distinct modes of action, or alternative pharmacological profiles.


    Organizational Affiliation

    Department of Structural Biology & Biophysics, Pfizer Groton Laboratories, Groton, Connecticut 06340, USA. shenping.liu@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholesteryl ester transfer protein
A
476Homo sapiensMutation(s): 6 
Gene Names: CETP
Find proteins for P11597 (Homo sapiens)
Go to Gene View: CETP
Go to UniProtKB:  P11597
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
0SF
Query on 0SF

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A
(2R)-3-{[4-(4-chloro-3-ethylphenoxy)pyrimidin-2-yl][3-(1,1,2,2-tetrafluoroethoxy)benzyl]amino}-1,1,1-trifluoropropan-2-ol
C24 H21 Cl F7 N3 O3
BTIIJGFMCVLCET-LJQANCHMSA-N
 Ligand Interaction
2OB
Query on 2OB

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A
CHOLESTERYL OLEATE
(3BETA,9BETA,14BETA,17ALPHA)-CHOLEST-5-EN-3-YL (9Z)-OCTADEC-9-ENOATE
C45 H78 O2
RJECHNNFRHZQKU-RMUVNZEASA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PCW
Query on PCW

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A
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
(Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.772α = 90.00
b = 69.915β = 90.00
c = 187.145γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-05-07 
  • Released Date: 2012-09-05 
  • Deposition Author(s): Liu, S., Qiu, X.

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references
  • Version 1.2: 2012-11-14
    Type: Database references