4OP1

GKRP bound to AMG0556 and Sorbitol-6-Phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 5. A Novel Aryl Sulfone Series, Optimization Through Conformational Analysis.

Tamayo, N.A., Norman, M.H., Bartberger, M.D., Hong, F.T., Bo, Y., Liu, L., Nishimura, N., Yang, K.C., Tadesse, S., Fotsch, C., Chen, J., Chmait, S., Cupples, R., Hale, C., Jordan, S.R., Lloyd, D.J., Sivits, G., Van, G., St Jean, D.J.

(2015) J Med Chem 58: 4462-4482

  • DOI: 10.1021/jm5018175
  • Primary Citation of Related Structures:  
    4OP1, 4OP2, 4OP3

  • PubMed Abstract: 

    • The glucokinase-glucokinase regulatory protein (GK-GKRP) complex plays an important role in controlling glucose homeostasis in the liver. We have recently disclosed a series of arylpiperazines as in vitro and in vivo disruptors of the GK-GKRP complex with efficacy in rodent models of type 2 diabetes mellitus (T2DM) ...

    The glucokinase-glucokinase regulatory protein (GK-GKRP) complex plays an important role in controlling glucose homeostasis in the liver. We have recently disclosed a series of arylpiperazines as in vitro and in vivo disruptors of the GK-GKRP complex with efficacy in rodent models of type 2 diabetes mellitus (T2DM). Herein, we describe a new class of aryl sulfones as disruptors of the GK-GKRP complex, where the central piperazine scaffold has been replaced by an aromatic group. Conformational analysis and exploration of the structure-activity relationships of this new class of compounds led to the identification of potent GK-GKRP disruptors. Further optimization of this novel series delivered thiazole sulfone 93, which was able to disrupt the GK-GKRP interaction in vitro and in vivo and, by doing so, increases cytoplasmic levels of unbound GK.

    Organizational Affiliation: 

    †Department of Therapeutic Discovery-Medicinal Chemistry, ‡Department of Therapeutic Discovery-Molecular Structure and Characterization, §Department of Metabolic Disorders, ∥Department of Pharmacokinetics and Drug Metabolism, and ⊥Department of Pathology, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase Regulatory Protein A, B638Homo sapiensMutation(s): 0 
Gene Names: GCKR
Find proteins for Q14397 (Homo sapiens)
Explore Q14397 
Go to UniProtKB:  Q14397
NIH Common Fund Data Resources
PHAROS:  Q14397
GTEx:  ENSG00000084734
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2UW
Query on 2UW
Download Ideal Coordinates CCD File 
A, B
(2S)-2-(6-{5-[(6-aminopyridin-3-yl)sulfonyl]thiophen-2-yl}-5-chloropyridin-3-yl)-1,1,1-trifluoropropan-2-ol
C17 H13 Cl F3 N3 O3 S2
KMKJDWRQGUEOJR-INIZCTEOSA-N		 Ligand Interaction
S6P
Query on S6P
Download Ideal Coordinates CCD File 
A, B
D-SORBITOL-6-PHOSPHATE
C6 H15 O9 P
GACTWZZMVMUKNG-SLPGGIOYSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.18α = 90
b = 149.18β = 90
c = 132.105γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references