3I60 | pdb_00003i60

Crystal structure of ERK2 bound to (S)-4-(2-(2-chlorophenylamino)-5-methylpyrimidin-4-yl)-N-(2-hydroxy-1-phenylethyl)-1H-pyrrole-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb3I60/pdb

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


• Deposited: 2009-07-06 Released: 2010-01-12 
• Deposition Author(s): Jacobs, M.D., Xie, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: other

Literature

Structure-guided design of potent and selective pyrimidylpyrrole inhibitors of extracellular signal-regulated kinase (ERK) using conformational control.

Aronov, A.M., Tang, Q., Martinez-Botella, G., Bemis, G.W., Cao, J., Chen, G., Ewing, N.P., Ford, P.J., Germann, U.A., Green, J., Hale, M.R., Jacobs, M., Janetka, J.W., Maltais, F., Markland, W., Namchuk, M.N., Nanthakumar, S., Poondru, S., Straub, J., ter Haar, E., Xie, X.

(2009) J Med Chem 52: 6362-6368

• PubMed: 19827834 
• DOI: https://doi.org/10.1021/jm900630q
• Primary Citation Related Structures: 
  3I4B, 3I5Z, 3I60


• PubMed Abstract: 
  

  The Ras/Raf/MEK/ERK signal transduction, an oncogenic pathway implicated in a variety of human cancers, is a key target in anticancer drug design. A novel series of pyrimidylpyrrole ERK inhibitors has been identified. Discovery of a conformational change for lead compound 2, when bound to ERK2 relative to antitarget GSK3, enabled structure-guided selectivity optimization, which led to the discovery of 11e, a potent, selective, and orally bioavailable inhibitor of ERK.

---

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.35 kDa 
• Atom Count: 2,910 
• Modeled Residue Count: 335 
• 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: ERK2, MAPK1, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E86	E [auth A]	4-{2-[(2-chlorophenyl)amino]-5-methylpyrimidin-4-yl}-N-[(1S)-2-hydroxy-1-phenylethyl]-1H-pyrrole-2-carboxamide C24 H22 Cl N5 O2 AICUOEJPCSKION-OAQYLSRUSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.248 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.061	α = 90
b = 70.251	β = 90
c = 119.598	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Jacobs, M.D., Xie, X.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description