Crystal Structure of ERK2 in complex with 2-(1H-pyrazol-4-yl)-5H-pyrrolo[2,3-b]pyrazine

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Fragment-based discovery of potent ERK2 pyrrolopyrazine inhibitors.

Burdick, D.J.Wang, S.Heise, C.Pan, B.Drummond, J.Yin, J.Goeser, L.Magnuson, S.Blaney, J.Moffat, J.Wang, W.Chen, H.

(2015) Bioorg Med Chem Lett 25: 4728-4732

  • DOI: https://doi.org/10.1016/j.bmcl.2015.08.048
  • Primary Citation of Related Structures:  
    4QP1, 4QP2, 4QP3, 4QP4, 4QP6, 4QP7, 4QP8, 4QP9, 4QPA

  • PubMed Abstract: 

    A fragment-based lead discovery approach was used to discover novel ERK2 inhibitors. The crystal structure of N-benzyl-9H-purin-6-amine 1 in complex with ERK2 elucidated its hinge-binding mode. In addition, the simultaneous binding of an imidazole molecule adjacent to 1 suggested a direction for fragment expansion. Structure-based core hopping applied to 1 led to 5H-pyrrolo[3,2-b]pyrazine (3) that afforded direct vectors to probe the pockets of interest while retaining the essential hinge binding elements. Utilizing the new vectors for SAR exploration, the new core 3 was quickly optimized to compound 39 resulting in a greater than 6600-fold improvement in potency.

  • Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, United States. Electronic address: burdick.dan@gene.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1
A, B
369Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
GTEx:  ENSG00000100030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 363

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C9 H7 N5
Binding Affinity Annotations 
IDSourceBinding Affinity
363 BindingDB:  4QP7 IC50: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.07α = 90
b = 67.36β = 102.27
c = 87.26γ = 90
Software Package:
Software NamePurpose
BOSdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations