4QP7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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 Computational Chemistry, Genentech, Inc., South San Francisco, CA 94080, United States. Electronic address: chen.huifen@gene.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A, B369Homo sapiensMutation(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 
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
363
Query on 363
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		2-(1H-pyrazol-4-yl)-5H-pyrrolo[2,3-b]pyrazine
C9 H7 N5
LTFQPYDMHBLAGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
363 Binding MOAD:  4QP7 IC50: 5900 (nM) from 1 assay(s)
BindingDB:  4QP7 IC50: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-06-22 
  • Released Date: 2015-09-23 
    • Deposition Author(s): Yin, J., Wang, W.

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