6CPW

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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).


    Organizational Affiliation

    Discovery Chemistry, Merck & Co., Inc., 2015 Galloping Hill Rd, Kenilworth, NJ 07033, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A366Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus)
Explore P63086 
Go to UniProtKB:  P63086
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8V (Subject of Investigation/LOI)
Query on F8V

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 71.341α = 90
b = 91.318β = 90
c = 63.289γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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