3TDC | pdb_00003tdc

Crystal Structure of Human Acetyl-CoA carboxylase 2

• PDB DOI: https://doi.org/10.2210/pdb3TDC/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-08-10 Released: 2011-10-12 
• Deposition Author(s): Dougan, D.R., Mol, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.218 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and structure-activity relationships of spirolactones bearing 2-ureidobenzothiophene as acetyl-CoA carboxylases inhibitors.

Yamashita, T., Kamata, M., Endo, S., Yamamoto, M., Kakegawa, K., Watanabe, H., Miwa, K., Yamano, T., Funata, M., Sakamoto, J., Tani, A., Mol, C.D., Zou, H., Dougan, D.R., Sang, B., Snell, G., Fukatsu, K.

(2011) Bioorg Med Chem Lett 21: 6314-6318

• PubMed: 21944854 
• DOI: https://doi.org/10.1016/j.bmcl.2011.08.117
• Primary Citation Related Structures: 
  3TDC


• PubMed Abstract: 
  

  The co-crystal structure of the human acetyl-coenzyme A 2 (ACC2) carboxyl transferase domain and the reported compound CP-640186 (1b) suggested that two carbonyl groups are essential for potent ACC2 inhibition. By focusing on enhancing the interactions between the two carbonyl groups and the amino acid residues Gly(2162) and Glu(2230), we used ligand- and structure-based drug design to discover spirolactones bearing a 2-ureidobenzothiophene moiety.

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Organizational Affiliation: 
• Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532-8686, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.1 kDa 
• Atom Count: 6,284 
• Modeled Residue Count: 720 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase 2 variant	A	762	Homo sapiens	Mutation(s): 0  EC: 6.4.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O00763 (Homo sapiens) Explore O00763  Go to UniProtKB:  O00763
PHAROS:  O00763 GTEx:  ENSG00000076555

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0EU	B [auth A]	1-[3-({4-[(5S)-3,3-dimethyl-1-oxo-2-oxa-7-azaspiro[4.5]dec-7-yl]piperidin-1-yl}carbonyl)-1-benzothiophen-2-yl]-3-ethylurea C27 H36 N4 O4 S DSUNZEZCXUMUEH-MHZLTWQESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0EU	BindingDB:  3TDC	IC50: min: 5.4, max: 13 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.218 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.921	α = 90
b = 119.756	β = 90
c = 146.035	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Dougan, D.R., Mol, C.D.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description