3TDC

Crystal Structure of Human Acetyl-CoA carboxylase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1016/j.bmcl.2011.08.117
  • Primary Citation of 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 interactio ...

    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.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532-8686, Japan. Yamashita_Tohru@takeda.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-CoA carboxylase 2 variantA762Homo sapiensMutation(s): 0 
Gene Names: ACACBACC2ACCB
EC: 6.4.1.2
Find proteins for O00763 (Homo sapiens)
Explore O00763 
Go to UniProtKB:  O00763
NIH Common Fund Data Resources
PHAROS  O00763
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0EU
Query on 0EU

Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0EUIC50:  13   nM  Binding MOAD
0EUIC50 :  5.400000095367432   nM  PDBBind
0EUIC50:  5.400000095367432   nM  BindingDB
0EUIC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.921α = 90
b = 119.756β = 90
c = 146.035γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references