5AX3

Crystal structure of ERK2 complexed with allosteric and ATP-competitive inhibitors.

• PDB DOI: https://doi.org/10.2210/pdb5AX3/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-07-14 Released: 2016-02-10 
• Deposition Author(s): Kinoshita, T., Sugiyama, H., Mori, Y., Takahashi, N., Tomonaga, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Identification of allosteric ERK2 inhibitors through in silico biased screening and competitive binding assay

Kinoshita, T., Sugiyama, H., Mori, Y., Takahashi, N., Tomonaga, A.

(2016) Bioorg Med Chem Lett 26: 955-958

• PubMed: 26733474 
• DOI: https://doi.org/10.1016/j.bmcl.2015.12.056
• Primary Citation of Related Structures:  
  5AX3


• PubMed Abstract: 
  

  Extracellular signal-regulated kinase 2 (ERK2) is a drug target for type 2 diabetes mellitus. A peptide-type ERK2 inhibitor (PEP) was discovered in the previous study through the knowledge-based method and showed physiological effects on the db/db mice model of type 2 diabetes. Here, the crystal structure showed that PEP bound to the allosteric site without the interruption of the ATP competitive inhibitor binding to ERK2. An in silico biased-screening using the focused library rendered three compounds with inhibitory activity of IC50 <100 μM. Among them, two compounds revealed the concentration-dependent competition with PEP and could be lead compounds for antidiabetic medicine.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: [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)

Macromolecule Content

• Total Structure Weight: 44.12 kDa 
• Atom Count: 2,831 
• Modelled Residue Count: 341 
• Deposited Residue Count: 380 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	368	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
allosteric and ATP-competitive inhibitor	B	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P40763 (Homo sapiens) Explore P40763  Go to UniProtKB:  P40763
PHAROS:  P40763 GTEx:  ENSG00000168610

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ID	C [auth A]	(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL C11 H13 I N4 O4 WHSIXKUPQCKWBY-IOSLPCCCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.835	α = 90
b = 66.465	β = 90
c = 116.871	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Kinoshita, T., Sugiyama, H., Mori, Y., Takahashi, N., Tomonaga, A.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description