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.,Department of Computational Chemistry, Genentech, Inc., South San Francisco, CA 94080, United States.,Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, United States.,Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, United States. Electronic address: wang.weiru@gene.com.,Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, United States. Electronic address: burdick.dan@gene.com.,Department of Biochemical Pharmacology, Genentech, Inc., South San Francisco, CA 94080, United States.,Department of Computational Chemistry, Genentech, Inc., South San Francisco, CA 94080, United States. Electronic address: chen.huifen@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