4MSU

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

• PDB DOI:  https://doi.org/10.2210/pdb4MSU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-18 Released: 2014-03-12 
• Deposition Author(s): 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.

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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 

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

• PubMed: 24405172 
• DOI: https://doi.org/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). 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 145.03 kDa 
• Atom Count: 9,262 
• Modelled Residue Count: 1,175 
• Deposited Residue Count: 1,272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase regulatory protein	A, B	636	Homo sapiens	Mutation(s): 0  Gene Names: GCKR
UniProt & NIH Common Fund Data Resources
Find proteins for Q14397 (Homo sapiens) Explore Q14397  Go to UniProtKB:  Q14397
PHAROS:  Q14397

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2EU	C [auth A], Q [auth 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
S6P	D [auth A], R [auth B]	D-SORBITOL-6-PHOSPHATE C6 H15 O9 P GACTWZZMVMUKNG-SLPGGIOYSA-N
IOD	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	EA [auth B], FA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2EU	BindingDB:  4MSU	Kd: 240 (nM) from 1 assay(s)
		IC50: 1420 (nM) from 1 assay(s)
		EC50: 3640 (nM) from 1 assay(s)
	Binding MOAD:  4MSU	IC50: 1420 (nM) from 1 assay(s)

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 = 148.427	α = 90
b = 148.427	β = 90
c = 132.069	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): 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.

Revision History  

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