4J1R

Crystal Structure of GSK3b in complex with inhibitor 15R

• PDB DOI: https://doi.org/10.2210/pdb4J1R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-02-01 Released: 2013-03-20 
• Deposition Author(s): Zhan, C., Wang, Y., Wach, J., Sheehan, P., Zhong, C., Harris, R., Patskovsky, Y., Bishop, J., Haggarty, S., Ramek, A., Berry, K., O'Herin, C., Koehler, A.N., Hung, A.W., Young, D.W., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Fragment-based approach using diversity-oriented synthesis yields a GSK3b inhibitor

Wang, Y., Wach, J., Sheehan, P., Zhong, C., Zhan, C., Harris, R., Almo, S.C., Bishop, J., Haggarty, S., Ramek, A., Berry, K., O'Herin, C., Koehler, A.N., Hung, A.W., Young, D.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 190.37 kDa 
• Atom Count: 11,248 
• Modelled Residue Count: 1,382 
• Deposited Residue Count: 1,696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B, C, D	424	Homo sapiens	Mutation(s): 0  Gene Names: GSK3B EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I5R	F [auth A], I [auth B], L [auth C], O [auth D]	(2R)-2-(1H-indol-3-ylmethyl)-1,4-dihydropyrido[2,3-b]pyrazin-3(2H)-one C16 H14 N4 O DNASGFXXJPEUMJ-CQSZACIVSA-N
PO4	E [auth A], H [auth B], K [auth C], N [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	G [auth A], J [auth B], M [auth C], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B, C, D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
I5R	BindingDB:  4J1R	Kd: 9000 (nM) from 1 assay(s)
		IC50: 1.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.516	α = 90.13
b = 67.441	β = 90.08
c = 116.422	γ = 81.11

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Zhan, C., Wang, Y., Wach, J., Sheehan, P., Zhong, C., Harris, R., Patskovsky, Y., Bishop, J., Haggarty, S., Ramek, A., Berry, K., O'Herin, C., Koehler, A.N., Hung, A.W., Young, D.W., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection