5X5O

Crystal structure of ZAK in complex with compound D2829

• PDB DOI: https://doi.org/10.2210/pdb5X5O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-02-17 Released: 2017-12-27 
• Deposition Author(s): Dai, Y.B., Zhao, P., Yun, C.H.
• Funding Organization(s): National Science Foundation of China, National Basic Research Program of China, Ministry of Science and Technology of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structure Based Design of N-(3-((1H-Pyrazolo[3,4-b]pyridin-5-yl)ethynyl)benzenesulfonamides as Selective Leucine-Zipper and Sterile-alpha Motif Kinase (ZAK) Inhibitors.

Chang, Y., Lu, X., Shibu, M.A., Dai, Y.B., Luo, J., Zhang, Y., Li, Y., Zhao, P., Zhang, Z., Xu, Y., Tu, Z.C., Zhang, Q.W., Yun, C.H., Huang, C.Y., Ding, K.

(2017) J Med Chem 60: 5927-5932

• PubMed: 28586211 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00572
• Primary Citation of Related Structures:  
  5X5O


• PubMed Abstract: 
  

  A series of N-(3-((1H-pyrazolo[3,4-b]pyridin-5-yl)ethynyl)benzenesulfonamides were designed as the first class of highly selective ZAK inhibitors. The representative compound 3h strongly inhibits the kinase activity of ZAK with an IC ₅₀ of 3.3 nM and dose-dependently suppresses the activation of ZAK downstream signals in vitro and in vivo, while it is significantly less potent for the majority of 403 nonmutated kinases evaluated. Compound 3h also exhibits orally therapeutic effects on cardiac hypertrophy in a spontaneous hypertensive rat model.

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Organizational Affiliation: 

State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Macao, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.86 kDa 
• Atom Count: 2,499 
• Modelled Residue Count: 291 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase MLT	A	310	Homo sapiens	Mutation(s): 0  Gene Names: ZAK, MLTK, HCCS4 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYL2 (Homo sapiens) Explore Q9NYL2  Go to UniProtKB:  Q9NYL2
PHAROS:  Q9NYL2 GTEx:  ENSG00000091436

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7Z0	B [auth A]	N-[2,4-bis(fluoranyl)-3-[2-(3-methoxy-1H-pyrazolo[3,4-b]pyridin-5-yl)ethynyl]phenyl]-3-bromanyl-benzenesulfonamide C21 H13 Br F2 N4 O3 S PJGQKTLXZJMPIM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7Z0	BindingDB:  5X5O	IC50: 5 (nM) from 1 assay(s)
	Binding MOAD:  5X5O	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.057	α = 90
b = 48.501	β = 105.48
c = 42.625	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Dai, Y.B., Zhao, P., Yun, C.H.

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Funding Organization	Location	Grant Number
National Science Foundation of China	China	31270769
National Basic Research Program of China	China	2012CB917202
Ministry of Science and Technology of China	China	NCET-12-0013

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references