Discovery of MK-8353: An Orally Bioavailable Dual Mechanism ERK Inhibitor for Oncology

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


MK-8353: Discovery of an Orally Bioavailable Dual Mechanism ERK Inhibitor for Oncology.

Boga, S.B.Deng, Y.Zhu, L.Nan, Y.Cooper, A.B.Shipps Jr., G.W.Doll, R.Shih, N.Y.Zhu, H.Sun, R.Wang, T.Paliwal, S.Tsui, H.C.Gao, X.Yao, X.Desai, J.Wang, J.Alhassan, A.B.Kelly, J.Patel, M.Muppalla, K.Gudipati, S.Zhang, L.K.Buevich, A.Hesk, D.Carr, D.Dayananth, P.Black, S.Mei, H.Cox, K.Sherborne, B.Hruza, A.W.Xiao, L.Jin, W.Long, B.Liu, G.Taylor, S.A.Kirschmeier, P.Windsor, W.T.Bishop, R.Samatar, A.A.

(2018) ACS Med Chem Lett 9: 761-767

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00220
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The emergence and evolution of new immunological cancer therapies has sparked a rapidly growing interest in discovering novel pathways to treat cancer. Toward this aim, a novel series of pyrrolidine derivatives (compound 5 ) were identified as potent inhibitors of ERK1/2 with excellent kinase selectivity and dual mechanism of action but suffered from poor pharmacokinetics (PK). The challenge of PK was overcome by the discovery of a novel 3( S )-thiomethyl pyrrolidine analog 7 . Lead optimization through focused structure-activity relationship led to the discovery of a clinical candidate MK-8353 suitable for twice daily oral dosing as a potential new cancer therapeutic.

  • Organizational Affiliation

    Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1366Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
Find proteins for P63086 (Rattus norvegicus)
Explore P63086 
Go to UniProtKB:  P63086
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63086
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G67 (Subject of Investigation/LOI)
Query on G67

Download Ideal Coordinates CCD File 
D [auth A](3S)-3-(methylsulfanyl)-1-(2-{4-[4-(1-methyl-1H-1,2,4-triazol-3-yl)phenyl]-3,6-dihydropyridin-1(2H)-yl}-2-oxoethyl)-N-(3-{6-[(propan-2-yl)oxy]pyridin-3-yl}-1H-indazol-5-yl)pyrrolidine-3-carboxamide
C37 H41 N9 O3 S
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
G67 BindingDB:  6DCG IC50: min: 7, max: 20 (nM) from 2 assay(s)
Binding MOAD:  6DCG IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.018α = 90
b = 91.173β = 90
c = 63.051γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description