1WZY | pdb_00001wzy

Crystal structure of human ERK2 complexed with a pyrazolopyridazine derivative

• PDB DOI: https://doi.org/10.2210/pdb1WZY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-03-10 Released: 2005-12-20 
• Deposition Author(s): Kinoshita, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.292 (Depositor) 
• R-Value Work: 
  0.249 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Literature

Crystal structure of human ERK2 complexed with a pyrazolo[3,4-c]pyridazine derivative

Kinoshita, T., Warizaya, M., Ohori, M., Sato, K., Neya, M., Fujii, T.

(2006) Bioorg Med Chem Lett 16: 55-58

• PubMed: 16242327 
• DOI: https://doi.org/10.1016/j.bmcl.2005.09.055
• Primary Citation Related Structures: 
  1WZY


• PubMed Abstract: 
  

  A series of pyrazolopyridazine compounds were briefly investigated as ERK2 inhibitors. The crystal structure of ERK2 complexed with an allyl derivative was determined. The compound induces structural change including movement of the glycine-rich loop and peptide flip between Met108-Glu109. As a result, the newly formed subsite can recognize small hydrophobic substituents but not hydrophilic ones.

---

Organizational Affiliation: 
• Exploratory Research Laboratories, Fujisawa Pharmaceutical Co., Ltd, 5-2-3 Tokodai, Tsukuba, Ibaraki 300-2698, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.6 kDa 
• Atom Count: 3,116 
• Modeled Residue Count: 350 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	368	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F29	B [auth A]	1-ALLYL-5-(2-PHENYLPYRAZOLO[1,5-A]PYRIDIN-3-YL)-1H-PYRAZOLO[3,4-C]PYRIDAZIN-3-AMINE C21 H17 N7 WHPQRPGHYADIAQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F29	BindingDB:  1WZY	IC50: 560 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.292 (Depositor) 
• R-Value Work:  0.249 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.599	α = 90
b = 68.541	β = 110.27
c = 59.833	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Kinoshita, T.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations