4O6E | pdb_00004o6e

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

• PDB DOI: https://doi.org/10.2210/pdb4O6E/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

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

• PubMed: 24813737 
• DOI: https://doi.org/10.1016/j.bmcl.2014.04.068
• Primary Citation 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.

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Organizational Affiliation: 
• Array BioPharma Inc, Boulder, CO 80301, USA. Electronic address: [e-mail].
Array BioPharma Inc, Boulder, CO 80301, USA.
Genentech Inc, 1 DNA Way, South San Francisco, CA 94080-4990, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.1 kDa 
• Atom Count: 2,925 
• Modeled Residue Count: 328 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	368	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2SH	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

Binding Affinity Annotations
ID	Source	Binding Affinity
2SH	BindingDB:  4O6E	Ki: 0.4 (nM) from 1 assay(s)
		IC50: min: 1, max: 45 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.85	α = 90
b = 65.766	β = 95
c = 52.654	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations