4XJ0 | pdb_00004xj0

Crystal structure of ERK2 in complex with an inhibitor 14K

• PDB DOI: https://doi.org/10.2210/pdb4XJ0/pdb

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


• Deposited: 2015-01-08 Released: 2015-09-16 
• Deposition Author(s): Yin, J., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.244 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Discovery of highly potent, selective, and efficacious small molecule inhibitors of ERK1/2.

Ren, L., Grina, J., Moreno, D., Blake, J.F., Gaudino, J.J., Garrey, R., Metcalf, A.T., Burkard, M., Martinson, M., Rasor, K., Chen, H., Dean, B., Gould, S.E., Pacheco, P., Shahidi-Latham, S., Yin, J., West, K., Wang, W., Moffat, J.G., Schwarz, J.B.

(2015) J Med Chem 58: 1976-1991

• PubMed: 25603482 
• DOI: https://doi.org/10.1021/jm501921k
• Primary Citation Related Structures: 
  4XJ0


• PubMed Abstract: 
  

  Using structure-based design, a novel series of pyridone ERK1/2 inhibitors was developed. Optimization led to the identification of (S)-14k, a potent, selective, and orally bioavailable agent that inhibited tumor growth in mouse xenograft models. On the basis of its in vivo efficacy and preliminary safety profiles, (S)-14k was selected for further preclinical evaluation.

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Organizational Affiliation: 
• Array BioPharma Inc, 3200 Walnut Street, Boulder, Colorado 80301, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 82.26 kDa 
• Atom Count: 5,788 
• Modeled Residue Count: 685 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A, B	349	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
41B	C [auth A], D [auth B]	1-[(1S)-1-(4-chloro-3-fluorophenyl)-2-hydroxyethyl]-4-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]pyridin-2(1H)-one C22 H22 Cl F N4 O3 PGGLRAWFUJMQBN-HXUWFJFHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A, B	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

Binding Affinity Annotations
ID	Source	Binding Affinity
41B	BindingDB:  4XJ0	Ki: 0.6 (nM) from 1 assay(s)
		IC50: min: 1.1, max: 3.9 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.244 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.191	α = 90
b = 83.191	β = 90
c = 274.493	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Yin, J., Wang, W.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description