Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 41.39 kDa 
• Atom Count: 3,032 
• Modelled Residue Count: 336 
• Deposited Residue Count: 352 
• Unique protein chains: 1

 5K4I

Crystal Structure of ERK2 in complex with compound 22

• PDB DOI:  https://doi.org/10.2210/pdb5K4I/pdb

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


• Deposited: 2016-05-20 Released: 2016-07-06 
• Deposition Author(s): Yin, J., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.232 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Discovery of (S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl)amino)pyrimidin-4-yl)pyridin-2(1H)-one (GDC-0994), an Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibitor in Early Clinical Development.

Blake, J.F., Burkard, M., Chan, J., Chen, H., Chou, K.J., Diaz, D., Dudley, D.A., Gaudino, J.J., Gould, S.E., Grina, J., Hunsaker, T., Liu, L., Martinson, M., Moreno, D., Mueller, L., Orr, C., Pacheco, P., Qin, A., Rasor, K., Ren, L., Robarge, K., Shahidi-Latham, S., Stults, J., Sullivan, F., Wang, W., Yin, J., Zhou, A., Belvin, M., Merchant, M., Moffat, J., Schwarz, J.B.

(2016) J Med Chem 59: 5650-5660

• PubMed: 27227380 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00389
• Primary Citation of Related Structures:  
  5K4I, 5K4J


• PubMed Abstract: 
  

The extracellular signal-regulated kinases ERK1/2 represent an essential node within the RAS/RAF/MEK/ERK signaling cascade that is commonly activated by oncogenic mutations in BRAF or RAS or by upstream oncogenic signaling. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. Simultaneous targeting of multiple nodes in the pathway, such as MEK and ERK, offers the prospect of enhanced efficacy as well as reduced potential for acquired resistance. Described herein is the discovery and characterization of GDC-0994 (22), an orally bioavailable small molecule inhibitor selective for ERK kinase activity.

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Organizational Affiliation: 

Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	352	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QB	B [auth A]	1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one C21 H18 Cl F N6 O2 RZUOCXOYPYGSKL-GOSISDBHSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6QB	BindingDB:  5K4I	Kd: 1.6 (nM) from 1 assay(s)
		IC50: min: 0.3, max: 140 (nM) from 11 assay(s)
	Binding MOAD:  5K4I	IC50: 3.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.232 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.668	α = 90
b = 71.333	β = 90
c = 119.529	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Yin, J., Wang, W.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release