5V4X | pdb_00005v4x

Human glucokinase in complex with novel pyrazole activator.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.250 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Discovery of potent and orally active 1,4-disubstituted indazoles as novel allosteric glucokinase activators.

Cheruvallath, Z.S., Gwaltney, S.L., Sabat, M., Tang, M., Wang, H., Jennings, A., Hosfield, D., Lee, B., Wu, Y., Halkowycz, P., Grimshaw, C.E.

(2017) Bioorg Med Chem Lett 27: 2678-2682

  • DOI: https://doi.org/10.1016/j.bmcl.2017.04.041
  • Primary Citation Related Structures: 
    5V4W, 5V4X

  • PubMed Abstract: 

    Guided by co-crystal structural information obtained from a different series we were exploring, a scaffold morphing and SBDD approach led to the discovery of the 1,4-disubstituted indazole series as a novel class of GKAs that potently activate GK in enzyme and cell assays. anti-diabetic OGTT efficacy was demonstrated with 29 in a rodent models of type 2 diabetes.

    • Organizational Affiliation: 
    • Takeda California, 10410 Science Center Drive, San Diego 92121, USA. Electronic address: zacharia.cheruvallath@takedasd.com.

Macromolecule Content 

  • Total Structure Weight: 52.42 kDa 
  • Atom Count: 3,551 
  • Modeled Residue Count: 420 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucokinase458Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.250 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.874α = 90
b = 77.855β = 90
c = 119.927γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Structure summary