Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 44.12 kDa 
• Atom Count: 2831 
• Residue Count: 341 
• Unique protein chains: 2

5AX3

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

• DOI: 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 

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: 10.1016/j.bmcl.2015.12.056
• Structures With Same Primary Citation


• 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: 

Next Generation Healthcare Innovation Center, Fujitsu Limited, 17-25, Shinkamata 1-chome, Ota-ku, Tokyo, Tokyo 144-8588, Japan.

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
allosteric and ATP-competitive inhibitor	B	12	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ID	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5ID	IC50:  1200   nM  BindingDB
5ID	Ki:  530   nM  BindingDB

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

• Deposited Date: 2015-07-14 
• 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