4QP2

Crystal Structure of ERKs in complex with 5-chlorobenzo[d]oxazol-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


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:  

  • 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 mo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A, B
369Homo sapiensMutation(s): 0 
Gene Names: MAPK1 (ERK2, PRKM1, PRKM2)
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Go to Gene View: MAPK1
Go to UniProtKB:  P28482
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
36R
Query on 36R

Download SDF File 
Download CCD File 
A
5-chloro-1,3-benzoxazol-2-amine
C7 H5 Cl N2 O
YGCODSQDUUUKIV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
A, B
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
36RKd: 940000 nM (100) BINDINGDB
36RKd: 940000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.724α = 90.00
b = 82.724β = 90.00
c = 277.554γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
BOSdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references