Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44115.40 
• Atom Count: 2831 
• Residue Count: 380 
• 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


• 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: 2.984 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 

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


• 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].

Macromolecules

Find similar proteins by: Sequence  |  Structure

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 Gene View: MAPK1 Go to UniProtKB:  P28482

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
allosteric and ATP-competitive inhibitor	B	12	Homo sapiens	Mutation(s): 0  Gene Names: STAT3 (APRF)
Find proteins for P40763 (Homo sapiens) Go to Gene View: STAT3 Go to UniProtKB:  P40763

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 5-IODOTUBERCIDIN C11 H13 I N4 O4 WHSIXKUPQCKWBY-IOSLPCCCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5ID	Ki: 530 nM (100) BINDINGDB
5ID	IC50: 1200 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.984 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 43.835	α = 90.00
b = 66.465	β = 90.00
c = 116.871	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
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