3I4B

Crystal structure of GSK3b in complex with a pyrimidylpyrrole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3I4B/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-07-01 Released: 2010-01-12 
• Deposition Author(s): Ter Haar, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

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 of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.06 kDa 
• Atom Count: 6,342 
• Modelled Residue Count: 706 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	414	Homo sapiens	Mutation(s): 0  Gene Names: GSK3B EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841  Go to UniProtKB:  P49841
PHAROS:  P49841 GTEx:  ENSG00000082701

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z48	C [auth A], D [auth B]	N-[(1S)-2-hydroxy-1-phenylethyl]-4-[5-methyl-2-(phenylamino)pyrimidin-4-yl]-1H-pyrrole-2-carboxamide C24 H23 N5 O2 PFHKAGAZRDERTK-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z48	BindingDB:  3I4B	Ki: 7 (nM) from 1 assay(s)
	PDBBind:  3I4B	Ki: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.75	α = 90
b = 86.1	β = 90
c = 178.29	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Ter Haar, E.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description