5VT1

Crystal Structure of the Human CAMKK2B bound to a thiadiazinone benzamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9JSClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

1,2,6-Thiadiazinones as Novel Narrow Spectrum Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CaMKK2) Inhibitors.

Asquith, C.R.M.Godoi, P.H.Counago, R.M.Laitinen, T.Scott, J.W.Langendorf, C.G.Oakhill, J.S.Drewry, D.H.Zuercher, W.J.Koutentis, P.A.Willson, T.M.Kalogirou, A.S.

(2018) Molecules 23

  • DOI: https://doi.org/10.3390/molecules23051221
  • Primary Citation of Related Structures:  
    5VT1

  • PubMed Abstract: 

    We demonstrate for the first time that 4 H -1,2,6-thiadiazin-4-one (TDZ) can function as a chemotype for the design of ATP-competitive kinase inhibitors. Using insights from a co-crystal structure of a 3,5-bis(arylamino)-4 H -1,2,6-thiadiazin-4-one bound to calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), several analogues were identified with micromolar activity through targeted displacement of bound water molecules in the active site. Since the TDZ analogues showed reduced promiscuity compared to their 2,4-dianilinopyrimidine counter parts, they represent starting points for development of highly selective kinase inhibitors.


  • Organizational Affiliation

    Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. chris.asquith@unc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase kinase 2291Homo sapiensMutation(s): 0 
Gene Names: CAMKK2CAMKKBKIAA0787
EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RR4 (Homo sapiens)
Explore Q96RR4 
Go to UniProtKB:  Q96RR4
PHAROS:  Q96RR4
GTEx:  ENSG00000110931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RR4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9JS
Query on 9JS

Download Ideal Coordinates CCD File 
B [auth A]4-({5-[(3-hydroxy-4-methylphenyl)amino]-4-oxo-4H-1,2,6-thiadiazin-3-yl}amino)benzamide
C17 H15 N5 O3 S
DHBUOVPLOHMOJE-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.454α = 90
b = 100.454β = 90
c = 69.674γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9JSClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/50724-5

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Structure summary
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.3: 2018-06-06
    Changes: Data collection, Database references
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description