3SAY | pdb_00003say

Crystal structure of human glycogen synthase kinase 3 beta (GSK3b) in complex with inhibitor 142

PDB DOI: https://doi.org/10.2210/pdb3SAY/pdb

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

Deposited: 2011-06-03 Released: 2012-06-13
Deposition Author(s): Mazanetz, M.P., Cheng, R.K.Y., Rowan, F., Laughton, C.A., Barker, J.J., Fischer, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.230 (Depositor), 0.225 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of human glycogen synthase kinase 3 beta (GSK3b) in complex with inhibitor 142

Cheng, R.K.Y., Rowan, F., Barker, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 97.65 kDa
Atom Count: 5,858
Modeled Residue Count: 696
Deposited Residue Count: 860
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	430	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OFT Query on OFT Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	(3Z)-N,N-diethyl-3-[(3E)-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-ylidene]-2-oxo-2,3-dihydro-1H-indole-5-sulfonamide C₂₀ H₂₀ N₄ O₄ S ZZYLNEHSVPINPK-LCLDVOFVSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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: 2.23 Å
R-Value Free: 0.230 (Depositor), 0.225 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 110.78	β = 97.08
c = 67.91	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2015-04-29
Changes: Non-polymer description
Version 1.2: 2016-12-07
Changes: Structure summary
Version 1.3: 2016-12-28
Changes: Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-12-06
Changes: Data collection
Version 1.6: 2024-11-06
Changes: Structure summary