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 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
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  • 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 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • 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

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Ligand Structure Quality Assessment 


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