5VT1 | pdb_00005vt1

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

• PDB DOI: https://doi.org/10.2210/pdb5VT1/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-15 Released: 2017-05-24 
• Deposition Author(s): Counago, R.M., Asquith, C.R.M., Arruda, P., Edwards, A.M., Gileadi, O., Kalogirou, A.S., Koutentis, P.A., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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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

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

• PubMed: 29783765 
• 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].
Department of Pharmacology, University of North Carolina at Chapel Hill, NC 27599, USA. [e-mail].
Structural Genomics Consortium, Universidade Estadual de Campinas-UNICAMP, Campinas, São Paulo 13083-886, Brazil. [e-mail].
Structural Genomics Consortium, Universidade Estadual de Campinas-UNICAMP, Campinas, São Paulo 13083-886, Brazil. [e-mail].
Center for Molecular and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Avenida Cândido Rondon 400, P. O. Box 6010, 13083-875 Campinas, São Paulo 13083-886, Brazil. [e-mail].
School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland. [e-mail].
St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia. [e-mail].
Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne 3000, Australia. [e-mail].
The Florey Institute of Neuroscience and Mental Health, Parkville 3052, Australia. [e-mail].
St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia. [e-mail].
St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy 3065, Australia. [e-mail].
Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne 3000, Australia. [e-mail].
Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].
Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].
Department of Chemistry, University of Cyprus, P. O. Box 20537, 1678 Nicosia, Cyprus. [e-mail].
Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].
Department of Chemistry, University of Cyprus, P. O. Box 20537, 1678 Nicosia, Cyprus. [e-mail].
Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenis Str., Engomi, P. O. Box 22006, 1516 Nicosia, Cyprus. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.52 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 265 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase kinase 2	A	291	Homo sapiens	Mutation(s): 0  Gene Names: CAMKK2, CAMKKB, KIAA0787 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JS	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	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 = 100.454	α = 90
b = 100.454	β = 90
c = 69.674	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Counago, R.M., Asquith, C.R.M., Arruda, P., Edwards, A.M., Gileadi, O., Kalogirou, A.S., Koutentis, P.A., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History  

• 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