5VJA | pdb_00005vja

Crystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in complex with a pyrazolo[3,4-d]pyrimidinone ligand (HS38)

• PDB DOI: https://doi.org/10.2210/pdb5VJA/pdb

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


• Deposited: 2017-04-19 Released: 2018-08-08 
• Deposition Author(s): Carlson, D.A., Singer, M.R., Sutherland, C., Redondo, C., Alexander, L., Hughes, P.F., Knapp, S., MacDonald, J.A., Haystead, T.A.J.
• Funding Organization(s): Mandel Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Targeting Pim Kinases and DAPK3 to Control Hypertension.

Carlson, D.A., Singer, M.R., Sutherland, C., Redondo, C., Alexander, L.T., Hughes, P.F., Knapp, S., Gurley, S.B., Sparks, M.A., MacDonald, J.A., Haystead, T.A.J.

(2018) Cell Chem Biol 25: 1195

• PubMed: 30033129 
• DOI: https://doi.org/10.1016/j.chembiol.2018.06.006
• Primary Citation Related Structures: 
  5VJA


• PubMed Abstract: 
  

  Sustained vascular smooth muscle hypercontractility promotes hypertension and cardiovascular disease. The etiology of hypercontractility is not completely understood. New therapeutic targets remain vitally important for drug discovery. Here we report that Pim kinases, in combination with DAPK3, regulate contractility and control hypertension. Using a co-crystal structure of lead molecule (HS38) in complex with DAPK3, a dual Pim/DAPK3 inhibitor (HS56) and selective DAPK3 inhibitors (HS94 and HS148) were developed to provide mechanistic insight into the polypharmacology of hypertension. In vitro and ex vivo studies indicated that Pim kinases directly phosphorylate smooth muscle targets and that Pim/DAPK3 inhibition, unlike selective DAPK3 inhibition, significantly reduces contractility. In vivo, HS56 decreased blood pressure in spontaneously hypertensive mice in a dose-dependent manner without affecting heart rate. These findings suggest including Pim kinase inhibition within a multi-target engagement strategy for hypertension management. HS56 represents a significant step in the development of molecularly targeted antihypertensive medications.

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Organizational Affiliation: 
• Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada.
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany.
Division of Nephrology, Department of Medicine, Duke University and Durham VA Medical Centers, Durham, NC 27710, USA.
Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 132.02 kDa 
• Atom Count: 9,163 
• Modeled Residue Count: 1,058 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 3	A, B, C, D	283	Homo sapiens	Mutation(s): 0  Gene Names: DAPK3, ZIPK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43293 (Homo sapiens) Explore O43293  Go to UniProtKB:  O43293
PHAROS:  O43293 GTEx:  ENSG00000167657

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUK	F [auth A], H [auth B], J [auth C], M [auth D]	(2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide C14 H12 Cl N5 O2 S NASYEGAVCTZSDO-SSDOTTSWSA-N
ILE	K [auth D]	ISOLEUCINE C6 H13 N O2 AGPKZVBTJJNPAG-WHFBIAKZSA-N
DMS	E [auth A], G [auth B], I [auth C], L [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.492	α = 90
b = 98.491	β = 90.07
c = 115.022	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Carlson, D.A., Singer, M.R., Sutherland, C., Redondo, C., Alexander, L., Hughes, P.F., Knapp, S., MacDonald, J.A., Haystead, T.A.J.

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Funding Organization	Location	Grant Number
Mandel Foundation	United States	--

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description