Crystal Structure of ERK2 in complex with compound 22

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1352Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6QB

Download Ideal Coordinates CCD File 
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
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 43.668α = 90
b = 71.333β = 90
c = 119.529γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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