6CPW | pdb_00006cpw

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 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6CPW

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2018.04.063
  • Primary Citation 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).


  • Organizational Affiliation
    • Discovery Chemistry, Merck & Co., Inc., 2015 Galloping Hill Rd, Kenilworth, NJ 07033, United States. Electronic address: sobhana.babu.boga@merck.com.

Macromolecule Content 

  • Total Structure Weight: 43.2 kDa 
  • Atom Count: 2,998 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1366Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.11.24
UniProt
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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F8V

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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.224 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
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

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
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description