4O6E

Discovery of 5,6,7,8-tetrahydropyrido[3,4-d]pyrimidine Inhibitors of Erk2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 5,6,7,8-tetrahydropyrido[3,4-d]pyrimidine inhibitors of Erk2.

Blake, J.F.Gaudino, J.J.De Meese, J.Mohr, P.Chicarelli, M.Tian, H.Garrey, R.Thomas, A.Siedem, C.S.Welch, M.B.Kolakowski, G.Kaus, R.Burkard, M.Martinson, M.Chen, H.Dean, B.Dudley, D.A.Gould, S.E.Pacheco, P.Shahidi-Latham, S.Wang, W.West, K.Yin, J.Moffat, J.Schwarz, J.B.

(2014) Bioorg Med Chem Lett 24: 2635-2639

  • DOI: 10.1016/j.bmcl.2014.04.068
  • Primary Citation of Related Structures:  
    4O6E

  • PubMed Abstract: 
  • The discovery and optimization of a series of tetrahydropyridopyrimidine based extracellular signal-regulated kinase (Erks) inhibitors discovered via HTS and structure based drug design is reported. The compounds demonstrate potent and selective inhibition of Erk2 and knockdown of phospho-RSK levels in HepG2 cells and tumor xenografts ...

    The discovery and optimization of a series of tetrahydropyridopyrimidine based extracellular signal-regulated kinase (Erks) inhibitors discovered via HTS and structure based drug design is reported. The compounds demonstrate potent and selective inhibition of Erk2 and knockdown of phospho-RSK levels in HepG2 cells and tumor xenografts.


    Organizational Affiliation

    Genentech Inc, 1 DNA Way, South San Francisco, CA 94080-4990, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A368Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
GTEx:  ENSG00000100030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SH
Query on 2SH

Download Ideal Coordinates CCD File 
B [auth A]N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]-2-(tetrahydro-2H-pyran-4-ylamino)-5,8-dihydropyrido[3,4-d]pyrimidine-7(6H)-carboxamide
C21 H25 Cl F N5 O3
QTZUMCMRRPENJM-LJQANCHMSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2SH BindingDB:  4O6E Ki: 0.4 (nM) from 1 assay(s)
IC50: min: 1, max: 45 (nM) from 2 assay(s)
Binding MOAD:  4O6E IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.85α = 90
b = 65.766β = 95
c = 52.654γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2013-12-20 
  • Released Date: 2014-05-21 
  • Deposition Author(s): Yin, J., Wang, W.

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references