4WZ8 | pdb_00004wz8

Crystal structure of human-yeast chimera acetyl coA carboxylase CT domain bound to Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.209 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4WZ8

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Decreasing the Rate of Metabolic Ketone Reduction in the Discovery of a Clinical Acetyl-CoA Carboxylase Inhibitor for the Treatment of Diabetes.

Griffith, D.A.Kung, D.W.Esler, W.P.Amor, P.A.Bagley, S.W.Beysen, C.Carvajal-Gonzalez, S.Doran, S.D.Limberakis, C.Mathiowetz, A.M.McPherson, K.Price, D.A.Ravussin, E.Sonnenberg, G.E.Southers, J.A.Sweet, L.J.Turner, S.M.Vajdos, F.F.

(2014) J Med Chem 57: 10512-10526

  • DOI: https://doi.org/10.1021/jm5016022
  • Primary Citation Related Structures: 
    4WYO, 4WZ8

  • PubMed Abstract: 

    Acetyl-CoA carboxylase (ACC) inhibitors offer significant potential for the treatment of type 2 diabetes mellitus (T2DM), hepatic steatosis, and cancer. However, the identification of tool compounds suitable to test the hypothesis in human trials has been challenging. An advanced series of spirocyclic ketone-containing ACC inhibitors recently reported by Pfizer were metabolized in vivo by ketone reduction, which complicated human pharmacology projections. We disclose that this metabolic reduction can be greatly attenuated through introduction of steric hindrance adjacent to the ketone carbonyl. Incorporation of weakly basic functionality improved solubility and led to the identification of 9 as a clinical candidate for the treatment of T2DM. Phase I clinical studies demonstrated dose-proportional increases in exposure, single-dose inhibition of de novo lipogenesis (DNL), and changes in indirect calorimetry consistent with increased whole-body fatty acid oxidation. This demonstration of target engagement validates the use of compound 9 to evaluate the role of DNL in human disease.


  • Organizational Affiliation
    • Worldwide Medicinal Chemistry, ‡Cardiovascular, Metabolic and Endocrine Diseases Research Unit, and ∥Clinical Research Statistics, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 175.22 kDa 
  • Atom Count: 12,728 
  • Modeled Residue Count: 1,396 
  • Deposited Residue Count: 1,538 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA carboxylaseA [auth B],
B [auth C]
769Saccharomyces cerevisiae S288CMutation(s): 9 
Gene Names: ACC1ABP2FAS3MTR7YNR016CN3175
EC: 6.4.1.2 (PDB Primary Data), 6.3.4.14 (PDB Primary Data)
UniProt
Find proteins for Q00955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00955 
Go to UniProtKB:  Q00955
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00955
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3W7

Query on 3W7



Download:Ideal Coordinates CCD File
C [auth B],
D [auth C]
1'-(2H-indazol-5-ylcarbonyl)-1-(propan-2-yl)-1,4-dihydrospiro[indazole-5,4'-piperidin]-7(6H)-one
C22 H25 N5 O2
BJMKYJZZEBEMKH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.209 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.52α = 90
b = 138.03β = 90
c = 184.83γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-12-10 
  • Deposition Author(s): Vajdos, F.F.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references