6DCG | pdb_00006dcg

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

• PDB DOI: https://doi.org/10.2210/pdb6DCG/pdb

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


• Deposited: 2018-05-06 Released: 2018-08-08 
• Deposition Author(s): Boga, S.B., Deng, Y., Zhu, L., Nan, Y., Cooper, A., Shipps Jr., G.W., Doll, R., Shih, N., Zhu, H., Sun, R., Wang, T., Paliwal, S., Tsui, H., Gao, X., Yao, X., Desai, J., Wang, J., Alhassan, A.B., Kelly, J., Patel, M., Muppalla, K., Gudipati, S., Zhang, L., Buevich, A., Hesk, D., Carr, D., Dayananth, P., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.199 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 30034615 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00220
• Primary Citation Related Structures: 
  6DCG


• 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.

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Organizational Affiliation: 
• Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.
Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, 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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.25 kDa 
• Atom Count: 3,001 
• Modeled Residue Count: 326 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	366	Rattus norvegicus	Mutation(s): 0  Gene Names: Mapk1, Erk2, Mapk, Prkm1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086  Go to UniProtKB:  P63086

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G67 (Subject of Investigation/LOI)	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 KPQQGHGDBBJGFA-QNGWXLTQSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.199 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.018	α = 90
b = 91.173	β = 90
c = 63.051	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Boga, S.B., Deng, Y., Zhu, L., Nan, Y., Cooper, A., Shipps Jr., G.W., Doll, R., Shih, N., Zhu, H., Sun, R., Wang, T., Paliwal, S., Tsui, H., Gao, X., Yao, X., Desai, J., Wang, J., Alhassan, A.B., Kelly, J., Patel, M., Muppalla, K., Gudipati, S., Zhang, L., Buevich, A., Hesk, D., Carr, D., Dayananth, P., 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.

Revision History  

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