4ISF

Human glucokinase in complex with novel activator (2S)-3-cyclohexyl-2-(6-fluoro-2,4-dioxo-1,4-dihydroquinazolin-3(2H)-yl)-N-(1,3-thiazol-2-yl)propanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, synthesis and SAR of novel glucokinase activators.

Cheruvallath, Z.S.Gwaltney, S.L.Sabat, M.Tang, M.Feng, J.Wang, H.Miura, J.Guntupalli, P.Jennings, A.Hosfield, D.Lee, B.Wu, Y.

(2013) Bioorg Med Chem Lett 23: 2166-2171

  • DOI: 10.1016/j.bmcl.2013.01.093
  • Primary Citation of Related Structures:  
    4ISF, 4ISG, 4ISE

  • PubMed Abstract: 
  • Guided by co-crystal structures of compounds 15, 22 and 30, an SBDD approach led to the discovery of the 6-methyl pyridone series as a novel class of GKAs that potently activate GK in enzyme and cell assays. Anti-diabetic OGTT efficacy was demonstrated w ...

    Guided by co-crystal structures of compounds 15, 22 and 30, an SBDD approach led to the discovery of the 6-methyl pyridone series as a novel class of GKAs that potently activate GK in enzyme and cell assays. Anti-diabetic OGTT efficacy was demonstrated with 54 in a mouse model of type 2 diabetes.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego, CA 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase A458Homo sapiensMutation(s): 0 
Gene Names: GCKHXK4 Isoform II
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
NIH Common Fund Data Resources
PHAROS:  P35557
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FX
Query on 1FX

Download Ideal Coordinates CCD File 
A
(2S)-3-cyclohexyl-2-(6-fluoro-2,4-dioxo-1,4-dihydroquinazolin-3(2H)-yl)-N-(1,3-thiazol-2-yl)propanamide
C20 H21 F N4 O3 S
FWNYYSSFAUKKJU-INIZCTEOSA-N
 Ligand Interaction
GLC
Query on GLC

Download Ideal Coordinates CCD File 
A
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1FXEC50:  3100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.381α = 90
b = 77.578β = 90
c = 119.12γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary