3IMX

Crystal Structure of human glucokinase in complex with a synthetic activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Investigation of functionally liver selective glucokinase activators for the treatment of type 2 diabetes.

Bebernitz, G.R.Beaulieu, V.Dale, B.A.Deacon, R.Duttaroy, A.Gao, J.Grondine, M.S.Gupta, R.C.Kakmak, M.Kavana, M.Kirman, L.C.Liang, J.Maniara, W.M.Munshi, S.Nadkarni, S.S.Schuster, H.F.Stams, T.St Denny, I.Taslimi, P.M.Vash, B.Caplan, S.L.

(2009) J Med Chem 52: 6142-6152

  • DOI: 10.1021/jm900839k
  • Primary Citation of Related Structures:  
    3IMX

  • PubMed Abstract: 
  • Type 2 diabetes is a polygenic disease which afflicts nearly 200 million people worldwide and is expected to increase to near epidemic levels over the next 10-15 years. Glucokinase (GK) activators are currently under investigation by a number of pharmaceutical companies with only a few reaching early clinical evaluation ...

    Type 2 diabetes is a polygenic disease which afflicts nearly 200 million people worldwide and is expected to increase to near epidemic levels over the next 10-15 years. Glucokinase (GK) activators are currently under investigation by a number of pharmaceutical companies with only a few reaching early clinical evaluation. A GK activator has the promise of potentially affecting both the beta-cells of the pancreas, by improving glucose sensitive insulin secretion, as well as the liver, by reducing uncontrolled glucose output and restoring post-prandial glucose uptake and storage as glycogen. Herein, we report our efforts on a sulfonamide chemotype with the aim to generate liver selective GK activators which culminated in the discovery of 3-cyclopentyl-N-(5-methoxy-thiazolo[5,4-b]pyridin-2-yl)-2-[4-(4-methyl-piperazine-1-sulfonyl)-phenyl]-propionamide (17c). This compound activated the GK enzyme (alphaK(a) = 39 nM) in vitro at low nanomolar concentrations and significantly reduced glucose levels during an oral glucose tolerance test in normal mice.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139, USA. greg.bebernitz@novartis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucokinaseA455Homo sapiensMutation(s): 0 
Gene Names: GCKhCG_1745191tcag7.801
EC: 2.7.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
PHAROS:  P35557
GTEx:  ENSG00000106633 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35557
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B84
Query on B84

Download Ideal Coordinates CCD File 
C [auth A](2R)-3-cyclopentyl-N-(5-methoxy[1,3]thiazolo[5,4-b]pyridin-2-yl)-2-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}propanamide
C26 H33 N5 O4 S2
GMGMDWSPSKXMJH-OAQYLSRUSA-N
 Ligand Interaction
GLC
Query on GLC

Download Ideal Coordinates CCD File 
B [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.5α = 90
b = 90.3β = 90
c = 116.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2009-08-11 
  • Released Date: 2009-10-06 
  • Deposition Author(s): Stams, T., Vash, B.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary