5V4W

Human glucokinase in complex with novel indazole activator.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of potent and orally active 1,4-disubstituted indazoles as novel allosteric glucokinase activators.

Cheruvallath, Z.S.Gwaltney, S.L.Sabat, M.Tang, M.Wang, H.Jennings, A.Hosfield, D.Lee, B.Wu, Y.Halkowycz, P.Grimshaw, C.E.

(2017) Bioorg. Med. Chem. Lett. 27: 2678-2682

  • DOI: 10.1016/j.bmcl.2017.04.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Guided by co-crystal structural information obtained from a different series we were exploring, a scaffold morphing and SBDD approach led to the discovery of the 1,4-disubstituted indazole series as a novel class of GKAs that potently activate GK in ...

    Guided by co-crystal structural information obtained from a different series we were exploring, a scaffold morphing and SBDD approach led to the discovery of the 1,4-disubstituted indazole series as a novel class of GKAs that potently activate GK in enzyme and cell assays. anti-diabetic OGTT efficacy was demonstrated with 29 in a rodent models of type 2 diabetes.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego 92121, USA. Electronic address: zacharia.cheruvallath@takedasd.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
458Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2
Find proteins for P35557 (Homo sapiens)
Go to Gene View: GCK
Go to UniProtKB:  P35557
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8WM
Query on 8WM

Download SDF File 
Download CCD File 
A
(2S)-2-[4-(cyclopropylsulfonyl)-1H-indazol-1-yl]-N-(5-fluoro-1,3-thiazol-2-yl)-3-(oxan-4-yl)propanamide
C21 H23 F N4 O4 S2
VFUKAAVEACENGY-KRWDZBQOSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.709α = 90.00
b = 78.873β = 90.00
c = 120.333γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description