2G01 | pdb_00002g01

Pyrazoloquinolones as Novel, Selective JNK1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2G01/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-10 Released: 2006-04-18 
• Deposition Author(s): Abad-Zapatero, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.354 (Depositor) 
• R-Value Work: 
  0.283 (Depositor) 
• R-Value Observed: 
  0.286 (Depositor) 

Starting Model: experimental

Literature

Synthesis and SAR of 1,9-dihydro-9-hydroxypyrazolo[3,4-b]quinolin-4-ones as novel, selective c-Jun N-terminal kinase inhibitors.

Liu, M., Xin, Z., Clampit, J.E., Wang, S., Gum, R.J., Haasch, D.L., Trevillyan, J.M., Abad-Zapatero, C., Fry, E.H., Sham, H.L., Liu, G.

(2006) Bioorg Med Chem Lett 16: 2590-2594

• PubMed: 16527482 
• DOI: https://doi.org/10.1016/j.bmcl.2006.02.046
• Primary Citation Related Structures: 
  2G01


• PubMed Abstract: 
  

  A novel class of 1,9-dihydro-9-hydroxypyrazolo[3,4-b]quinolin-4-ones as c-Jun-N-terminal kinase (JNK) inhibitors is described. These compounds were synthesized via the condensation of 2-nitrobenzaldehydes and hydroxypyrazoles. The structure-activity relationships (SAR) and kinase selectivity profile of the inhibitors are also discussed. Compound 16 was identified as a potent JNK inhibitor with good cellular potency.

---

Organizational Affiliation: 
• Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6098, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.44 kDa 
• Atom Count: 5,918 
• Modeled Residue Count: 733 
• Deposited Residue Count: 762 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A, C [auth B]	370	Homo sapiens	Mutation(s): 2  Gene Names: MAPK8, JNK1, PRKM8 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983  Go to UniProtKB:  P45983
PHAROS:  P45983 GTEx:  ENSG00000107643

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-jun-amino-terminal kinase-interacting protein 1	B [auth F], D [auth G]	11	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF2 (Homo sapiens) Explore Q9UQF2  Go to UniProtKB:  Q9UQF2
PHAROS:  Q9UQF2 GTEx:  ENSG00000121653

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
73Q	G [auth A], J [auth B]	6-CHLORO-9-HYDROXY-1,3-DIMETHYL-1,9-DIHYDRO-4H-PYRAZOLO[3,4-B]QUINOLIN-4-ONE C12 H10 Cl N3 O2 AYKGPCNWPACUQV-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
73Q	BindingDB:  2G01	IC50: 1220 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.354 (Depositor) 
• R-Value Work:  0.283 (Depositor) 
• R-Value Observed: 0.286 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.622	α = 90
b = 150.622	β = 90
c = 118.996	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
SDMS	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Abad-Zapatero, C.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description