2OJI

Crystal structure of ERK2 in complex with N-benzyl-4-(4-(3-chlorophenyl)-1H-pyrazol-3-yl)-1H-pyrrole-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb2OJI/pdb

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


• Deposited: 2007-01-12 Released: 2007-02-06 
• Deposition Author(s): Xie, X., Jacobs, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 

Literature

Flipped Out: Structure-Guided Design of Selective Pyrazolylpyrrole ERK Inhibitors.

Aronov, A.M., Baker, C., Bemis, G.W., Cao, J., Chen, G., Ford, P.J., Germann, U.A., Green, J., Hale, M.R., Jacobs, M., Janetka, J.W., Maltais, F., Martinez-Botella, G., Namchuk, M.N., Straub, J., Tang, Q., Xie, X.

(2007) J Med Chem 50: 1280-1287

• PubMed: 17300186 
• DOI: https://doi.org/10.1021/jm061381f
• Primary Citation of Related Structures:  
  2OJG, 2OJI, 2OJJ, 2OK1


• PubMed Abstract: 
  

  The Ras/Raf/MEK/ERK signal transduction is a key oncogenic pathway implicated in a variety of human cancers. We have identified a novel series of pyrazolylpyrroles as inhibitors of ERK. Aided by the discovery of two distinct binding modes for the pyrazolylpyrrole scaffold, structure-guided optimization culminated in the discovery of 6p, a potent and selective inhibitor of ERK.

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Organizational Affiliation: 

Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, Massachusetts 02139-4242, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.09 kDa 
• Atom Count: 2,941 
• Modelled Residue Count: 344 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	380	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
33A	C [auth A]	N-BENZYL-4-[4-(3-CHLOROPHENYL)-1H-PYRAZOL-3-YL]-1H-PYRROLE-2-CARBOXAMIDE C21 H17 Cl N4 O PDJZASCRQRBYQS-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
33A	BindingDB:  2OJI	Ki: min: 85, max: 86 (nM) from 2 assay(s)
	PDBBind:  2OJI	Ki: 86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.557	α = 90
b = 69.675	β = 109.36
c = 59.986	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Xie, X., Jacobs, M.D.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations