5V4W | pdb_00005v4w

Human glucokinase in complex with novel indazole activator.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.261 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5V4W

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: 52.16 kDa 
  • Atom Count: 3,569 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8WM

Query on 8WM


Download:Ideal Coordinates CCD File
C [auth A](2S)-2-[4-(cyclopropylsulfonyl)-1H-indazol-1-yl]-N-(5-fluoro-1,3-thiazol-2-yl)-3-(oxan-4-yl)propanamide
C21 H23 F N4 O4 S2
VFUKAAVEACENGY-KRWDZBQOSA-N
GLC

Query on GLC


Download:Ideal Coordinates CCD File
B [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
IOD

Query on IOD


Download:Ideal Coordinates CCD File
D [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
8WM BindingDB:  5V4W EC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.261 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.709α = 90
b = 78.873β = 90
c = 120.333γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
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