7B6F | pdb_00007b6f

GSK3-beta in complex with compound (S)-5c

• PDB DOI: https://doi.org/10.2210/pdb7B6F/pdb

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


• Deposited: 2020-12-07 Released: 2020-12-16 
• Deposition Author(s): Tesch, R., Andreev, S., Koch, P., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

GSK3-beta in complex with compound (S)-5c

Tesch, R., Andreev, S., Koch, P., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.37 kDa 
• Atom Count: 2,928 
• Modeled Residue Count: 347 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A	365	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
SZW (Subject of Investigation/LOI)	B [auth A]	3-[(3~{S})-3-[(7-chloranyl-9~{H}-pyrimido[4,5-b]indol-4-yl)-methyl-amino]piperidin-1-yl]propanenitrile C19 H21 Cl N6 DLORPOXOKVMFDB-AWEZNQCLSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
SZW	BindingDB:  7B6F	IC50: min: 489, max: 501 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.692	α = 90
b = 63.191	β = 97.408
c = 132.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data processing
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Tesch, R., Andreev, S., Koch, P., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	397659447

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary