3TV5

Crystal Structure of the humanized carboxyltransferase domain of yeast Acetyl-coA caroxylase in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided Inhibitor Design for Human Acetyl-coenzyme A Carboxylase by Interspecies Active Site Conversion.

Rajamohan, F.Marr, E.Reyes, A.R.Landro, J.A.Anderson, M.D.Corbett, J.W.Dirico, K.J.Harwood, J.H.Tu, M.Vajdos, F.F.

(2011) J.Biol.Chem. 286: 41510-41519

  • DOI: 10.1074/jbc.M111.275396
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of acetyl-CoA carboxylases (ACCs), a crucial enzyme for fatty acid metabolism, has been shown to promote fatty acid oxidation and reduce body fat in animal models. Therefore, ACCs are attractive targets for structure-based inhibitor design ...

    Inhibition of acetyl-CoA carboxylases (ACCs), a crucial enzyme for fatty acid metabolism, has been shown to promote fatty acid oxidation and reduce body fat in animal models. Therefore, ACCs are attractive targets for structure-based inhibitor design, particularly the carboxyltransferase (CT) domain, which is the primary site for inhibitor interaction. We have cloned, expressed, and purified the CT domain of human ACC2 using baculovirus-mediated insect cell expression system. However, attempts to crystallize the human ACC2 CT domain have not been successful in our hands. Hence, we have been using the available crystal structure of yeast CT domain to design human ACC inhibitors. Unfortunately, as the selectivity of the lead series has increased against the full-length human enzyme, the potency against the yeast enzyme has decreased significantly. This loss of potency against the yeast enzyme correlated with a complete lack of binding of the human-specific compounds to crystals of the yeast CT domain. Here, we address this problem by converting nine key active site residues of the yeast CT domain to the corresponding human residues. The resulting humanized yeast ACC-CT (yCT-H9) protein exhibits biochemical and biophysical properties closer to the human CT domain and binding to human specific compounds. We report high resolution crystal structures of yCT-H9 complexed with inhibitors that show a preference for the human CT domain. These structures offer insights that explain the species selectivity of ACC inhibitors and may guide future drug design programs.


    Organizational Affiliation

    Pfizer Global Research and Development, Groton, Connecticut 06340, USA. francis.rajamohan@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl-CoA carboxylase
A, B, C
769Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 9 
Gene Names: ACC1 (ABP2, FAS3, MTR7)
EC: 6.4.1.2
Find proteins for Q00955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00955
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RCP
Query on RCP

Download SDF File 
Download CCD File 
A, B, C
(3R)-1'-(9-ANTHRYLCARBONYL)-3-(MORPHOLIN-4-YLCARBONYL)-1,4'-BIPIPERIDINE
C30 H35 N3 O3
LDQKDRLEMKIYMC-XMMPIXPASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RCPKd: 4800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 246.500α = 90.00
b = 123.114β = 94.24
c = 146.440γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Database references