5CTB

Humanized yeast ACC carboxyltransferase domain bound to 6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.199 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 57JClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of spirocyclic-diamine inhibitors of mammalian acetyl CoA-carboxylase.

Kung, D.W.Griffith, D.A.Esler, W.P.Vajdos, F.F.Mathiowetz, A.M.Doran, S.D.Amor, P.A.Bagley, S.W.Banks, T.Cabral, S.Ford, K.Garcia-Irizarry, C.N.Landis, M.S.Loomis, K.McPherson, K.Niosi, M.Rockwell, K.L.Rose, C.Smith, A.C.Southers, J.A.Tapley, S.Tu, M.Valentine, J.J.

(2015) Bioorg Med Chem Lett 25: 5352-5356

  • DOI: https://doi.org/10.1016/j.bmcl.2015.09.035
  • Primary Citation of Related Structures:  
    5CTB, 5CTC, 5CTE

  • PubMed Abstract: 

    A novel series of spirocyclic-diamine based, isoform non-selective inhibitors of acetyl-CoA carboxylase (ACC) is described. These spirodiamine derivatives were discovered by design of a library to mimic the structural rigidity and hydrogen-bonding pattern observed in the co-crystal structure of spirochromanone inhibitor I. The lead compound 3.5.1 inhibited de novo lipogenesis in rat hepatocytes, with an IC50 of 0.30 μM.


  • Organizational Affiliation

    Worldwide Medicinal Chemistry, Groton, CT 06340, United States. Electronic address: daniel.w.kung@pfizer.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA carboxylase
A, B, C
769Saccharomyces cerevisiaeMutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
57J
Query on 57J

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth C]
6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one
C24 H25 N3 O3
PQQBCUZITMWICX-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth C],
J [auth C],
K [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 245.853α = 90
b = 124.381β = 94.39
c = 145.674γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 57JClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2015-10-14 
  • Deposition Author(s): Vajdos, F.F.

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations