4MSU

Human GKRP bound to AMG-6861 and Sorbitol-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 1. Discovery of a Novel Tool Compound for in Vivo Proof-of-Concept.

Ashton, K.S.Andrews, K.L.Bryan, M.C.Chen, J.Chen, K.Chen, M.Chmait, S.Croghan, M.Cupples, R.Fotsch, C.Helmering, J.Jordan, S.R.Kurzeja, R.J.Michelsen, K.Pennington, L.D.Poon, S.F.Sivits, G.Van, G.Vonderfecht, S.L.Wahl, R.C.Zhang, J.Lloyd, D.J.Hale, C.St Jean, D.J.

(2014) J Med Chem 57: 309-324

  • DOI: 10.1021/jm4016735
  • Primary Citation of Related Structures:  
    4MSU

  • PubMed Abstract: 
  • Small molecule activators of glucokinase have shown robust efficacy in both preclinical models and humans. However, overactivation of glucokinase (GK) can cause excessive glucose turnover, leading to hypoglycemia. To circumvent this adverse side effect, we chose to modulate GK activity by targeting the endogenous inhibitor of GK, glucokinase regulatory protein (GKRP) ...

    Small molecule activators of glucokinase have shown robust efficacy in both preclinical models and humans. However, overactivation of glucokinase (GK) can cause excessive glucose turnover, leading to hypoglycemia. To circumvent this adverse side effect, we chose to modulate GK activity by targeting the endogenous inhibitor of GK, glucokinase regulatory protein (GKRP). Disrupting the GK-GKRP complex results in an increase in the amount of unbound cytosolic GK without altering the inherent kinetics of the enzyme. Herein we report the identification of compounds that efficiently disrupt the GK-GKRP interaction via a previously unknown binding pocket. Using a structure-based approach, the potency of the initial hit was improved to provide 25 (AMG-1694). When dosed in ZDF rats, 25 showed both a robust pharmacodynamic effect as well as a statistically significant reduction in glucose. Additionally, hypoglycemia was not observed in either the hyperglycemic or normal rats.


    Organizational Affiliation

    Department of Therapeutic Discovery-Medicinal Chemistry, ‡Department of Therapeutic Discovery-Molecular Structure and Characterization, §Department of Therapeutic Discovery-Protein Technologies, ∥Department of Metabolic Disorders, ⊥Department of Pharmacokinetics and Drug Metabolism, #Department of Pathology, Amgen, Inc. , One Amgen Center Drive, Thousand Oaks, California 91320-1799, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase regulatory protein AB636Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2EU
Query on 2EU

Download Ideal Coordinates CCD File 
A, B
1,1,1,3,3,3-hexafluoro-2-{4-[4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol
C17 H16 F6 N2 O3 S2
FTXKDYBMOPKENQ-UHFFFAOYSA-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 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2EUEC50:  3640   nM  BindingDB
2EUKd:  240   nM  BindingDB
2EUIC50:  1420   nM  Binding MOAD
2EUIC50:  1420   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.427α = 90
b = 148.427β = 90
c = 132.069γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release