5OY4 | pdb_00005oy4

GSK3beta complex with N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide

PDB DOI: https://doi.org/10.2210/pdb5OY4/pdb

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

Deposited: 2017-09-07 Released: 2017-11-01
Deposition Author(s): Bax, B.D., Convery, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.229 (Depositor), 0.223 (DCC)
R-Value Work:
0.194 (Depositor), 0.193 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome.

Henley, Z.A., Bax, B.D., Inglesby, L.M., Champigny, A., Gaines, S., Faulder, P., Le, J., Thomas, D.A., Washio, Y., Baldwin, I.R.

(2017) ACS Med Chem Lett 8: 1093-1098

PubMed: 29057057 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.7b00296
Primary Citation Related Structures:
5OY4, 6AYD

PubMed Abstract:
Selective inhibitors of phosphoinositide 3-kinase delta are of interest for the treatment of inflammatory diseases. Initial optimization of a 3-substituted indazole hit compound targeting the kinase PIM1 focused on improving selectivity over GSK3β through consideration of differences in the ATP binding pockets. Continued kinase cross-screening showed PI3Kδ activity in a series of 4,6-disubstituted indazole compounds, and subsequent structure-activity relationship exploration led to the discovery of an indole-containing lead compound as a potent PI3Kδ inhibitor with selectivity over the other PI3K isoforms.

Organizational Affiliation

Refractory Respiratory Inflammation DPU, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, U.K.

Macromolecule Content

Total Structure Weight: 152.98 kDa
Atom Count: 5,988
Modeled Residue Count: 753
Deposited Residue Count: 1,398
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	420	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene FRAT1	C [auth X], D [auth Y]	279	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92837 (Homo sapiens) Explore Q92837 Go to UniProtKB: Q92837
PHAROS: Q92837 GTEx: ENSG00000165879
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92837
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B4K Query on B4K Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	H [auth A], J [auth B]	~{N}-[6-[3,4-bis(oxidanyl)phenyl]-1~{H}-pyrazolo[3,4-b]pyridin-3-yl]ethanamide C₁₄ H₁₂ N₄ O₃ ZIVJGKMCTSKCAR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.229 (Depositor), 0.223 (DCC)
R-Value Work: 0.194 (Depositor), 0.193 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.686	α = 90
b = 152.686	β = 90
c = 212.29	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Bax, B.D.

Convery, M.A.

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary