7T78

CRYSTAL STRUCTURE OF GLUCOKINASE (HEXOKINASE 4) COMPLEXED WITH LIGAND DIETHYL ({2-[3-(4-METHANESULFONYLPHENO XY)-5-{[(2S)-1-METHOXYPROPAN-2-YL]OXY}BENZAMIDO]-1,3-THIAZ OL-4-YL}METHYL)PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Partial Glucokinase Activator Clinical Candidate: Diethyl ((3-(3-((5-(Azetidine-1-carbonyl)pyrazin-2-yl)oxy)-5-isopropoxybenzamido)-1 H -pyrazol-1-yl)methyl)phosphonate (BMS-820132).

Shi, Y.Wang, Y.Meng, W.Brigance, R.P.Ryono, D.E.Bolton, S.Zhang, H.Chen, S.Smirk, R.Tao, S.Tino, J.A.Williams, K.N.Sulsky, R.Nielsen, L.Ellsworth, B.Wong, M.K.Y.Sun, J.H.Leith, L.W.Sun, D.Wu, D.R.Gupta, A.Rampulla, R.Mathur, A.Chen, B.C.Wang, A.Fuentes-Catanio, H.G.Kunselman, L.Cap, M.Zalaznick, J.Ma, X.Liu, H.Taylor, J.R.Zebo, R.Jones, B.Kalinowski, S.Swartz, J.Staal, A.O'Malley, K.Kopcho, L.Muckelbauer, J.K.Krystek Jr., S.R.Spronk, S.A.Marcinkeviciene, J.Everlof, G.Chen, X.Q.Xu, C.Li, Y.X.Langish, R.A.Yang, Y.Wang, Q.Behnia, K.Fura, A.Janovitz, E.B.Pannacciulli, N.Griffen, S.Zinker, B.A.Krupinski, J.Kirby, M.Whaley, J.Zahler, R.Barrish, J.C.Robl, J.A.Cheng, P.T.W.

(2022) J Med Chem 65: 4291-4317

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02110
  • Primary Citation of Related Structures:  
    7T78, 7T79

  • PubMed Abstract: 

    Glucokinase (GK) is a key regulator of glucose homeostasis, and its small-molecule activators represent a promising opportunity for the treatment of type 2 diabetes. Several GK activators have been advanced into clinical trials and have demonstrated promising efficacy; however, hypoglycemia represents a key risk for this mechanism. In an effort to mitigate this hypoglycemia risk while maintaining the efficacy of the GK mechanism, we have investigated a series of amino heteroaryl phosphonate benzamides as ''partial" GK activators. The structure-activity relationship studies starting from a "full GK activator" 11 , which culminated in the discovery of the "partial GK activator" 31 (BMS-820132), are discussed. The synthesis and in vitro and in vivo preclinical pharmacology profiles of 31 and its pharmacokinetics (PK) are described. Based on its promising in vivo efficacy and preclinical ADME and safety profiles, 31 was advanced into human clinical trials.


  • Organizational Affiliation

    Fibrosis Chemistry, Small Molecule Drug Discovery, Research & Early Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543-4000, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Hexokinase-4
A, B
466Homo sapiensMutation(s): 0 
Gene Names: GCK
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G2T (Subject of Investigation/LOI)
Query on G2T

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
diethyl {[2-(3-[4-(methanesulfonyl)phenoxy]-5-{[(2S)-1-methoxypropan-2-yl]oxy}benzamido)-1,3-thiazol-4-yl]methyl}phosphonate
C26 H33 N2 O9 P S2
OQUMCVQSAWPKMT-SFHVURJKSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.37α = 90
b = 83.7β = 100.38
c = 84.97γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection