6CPW

Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology

• PDB DOI:  https://doi.org/10.2210/pdb6CPW/pdb

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-14 Released: 2018-05-23 
• Deposition Author(s): Hruza, A., Hruza, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology.

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

(2018) Bioorg Med Chem Lett 28: 2029-2034

• PubMed: 29748051 
• DOI: https://doi.org/10.1016/j.bmcl.2018.04.063
• Primary Citation of Related Structures:  
  6CPW


• PubMed Abstract: 
  

Compound 5 (SCH772984) was identified as a potent inhibitor of ERK1/2 with excellent selectivity against a panel of kinases (0/231 kinases tested @ 100 nM) and good cell proliferation activity, but suffered from poor PK (rat AUC PK @10 mpk = 0 μM h; F% = 0) which precluded further development. In an effort to identify novel ERK inhibitors with improved PK properties with respect to 5, a systematic exploration of sterics and composition at the 3-position of the pyrrolidine led to the discovery of a novel 3(S)-thiomethyl pyrrolidine analog 28 with vastly improved PK (rat AUC PK @10 mpk = 26 μM h; F% = 70).

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Organizational Affiliation: 

Discovery Chemistry, Merck & Co., Inc., 2015 Galloping Hill Rd, Kenilworth, NJ 07033, 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: 43.2 kDa 
• Atom Count: 2,998 
• Modelled Residue Count: 328 
• 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
F8V	D [auth A]	(3S)-N-[3-(4-fluorophenyl)-1H-indazol-5-yl]-3-(methylsulfanyl)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)pyrrolidine-3-carboxamide C35 H35 F N8 O2 S MRHUCFAJTNKMCG-DHUJRADRSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
F8V	Binding MOAD:  6CPW	IC50: 5.6 (nM) from 1 assay(s)
	BindingDB:  6CPW	IC50: min: 5.6, max: 25 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.224 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.341	α = 90
b = 91.318	β = 90
c = 63.289	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Hruza, A., Hruza, A.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references