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 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl-CoA carboxylase 2 variant
A
762Homo sapiensMutation(s): 0 
Gene Names: ACACB (ACC2, ACCB)
EC: 6.4.1.2
Find proteins for O00763 (Homo sapiens)
Go to Gene View: ACACB
Go to UniProtKB:  O00763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0EU
Query on 0EU

Download SDF File 
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: 5.4 - 13 nM (99) BINDINGDB
0EUIC50: 13 nM BINDINGMOAD
0EUIC50: 5.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 113.921α = 90.00
b = 119.756β = 90.00
c = 146.035γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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