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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I5R Query on I5R Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	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		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain E [auth A] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on 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)
I5R	BindingDB: 4J1R	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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
Version 1.4: 2024-11-06
Changes: Structure summary

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Help and Resources

4J1R

Crystal Structure of GSK3b in complex with inhibitor 15R

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)