3H0Q

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with compound 3

• PDB DOI: https://doi.org/10.2210/pdb3H0Q/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-10 Released: 2010-04-21 
• Deposition Author(s): Zhang, H., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 

Literature

Discovery of small molecule isozyme non-specific inhibitors of mammalian acetyl-CoA carboxylase 1 and 2.

Corbett, J.W., Freeman-Cook, K.D., Elliott, R., Vajdos, F., Rajamohan, F., Kohls, D., Marr, E., Zhang, H., Tong, L., Tu, M., Murdande, S., Doran, S.D., Houser, J.A., Song, W., Jones, C.J., Coffey, S.B., Buzon, L., Minich, M.L., Dirico, K.J., Tapley, S., McPherson, R.K., Sugarman, E., Harwood, H.J., Esler, W.

(2010) Bioorg Med Chem Lett 20: 2383-2388

• PubMed: 20219367 
• DOI: https://doi.org/10.1016/j.bmcl.2009.04.091
• Primary Citation of Related Structures:  
  3H0J, 3H0Q, 3H0S


• PubMed Abstract: 
  

  Screening Pfizer's compound library resulted in the identification of weak acetyl-CoA carboxylase inhibitors, from which were obtained rACC1 CT-domain co-crystal structures. Utilizing HTS hits and structure-based drug discovery, a more rigid inhibitor was designed and led to the discovery of sub-micromolar, spirochromanone non-specific ACC inhibitors. Low nanomolar, non-specific ACC-isozyme inhibitors that exhibited good rat pharmacokinetics were obtained from this chemotype.

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Organizational Affiliation: 

Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 263.13 kDa 
• Atom Count: 16,890 
• Modelled Residue Count: 2,021 
• Deposited Residue Count: 2,307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase	A, B, C	769	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: FAS3, ACC1, YNR016C, N3175 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B37	D [auth A], E [auth B], F [auth C]	4-({4-[(2-methylquinolin-6-yl)methyl]piperidin-1-yl}carbonyl)-2-phenylquinoline C32 H29 N3 O OZINPIJMBCNUEN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B37	PDBBind:  3H0Q	IC50: 842 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 246.953	α = 90
b = 124.248	β = 94.229
c = 145.271	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Zhang, H., Tong, L.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations