9X2Y: GSK3beta

GSK3beta complexed with BiS-8. Determined by X-ray diffraction at 1.96 Å resolution. Released 31 Dec 2025.

Method: X-ray diffraction
Resolution: 1.96 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 6,152
Mol. weight: 86.23 kDa
Ligands: MLI
Released: 31 Dec 2025

Explore 9X2Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9X2Y contains 45 α-helices and 28 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	38-44	7	1
β-strand	52-65	14	1
β-strand	68-75	8	1
β-strand	81-86	6	1
α-helix	96-103	8
β-strand	109	1	2
β-strand	112-118	7	1
β-strand	127-133	7	1
β-strand	137-138	2	2
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-174	20
β-strand	177-178	2	3
α-helix	184-186	3
β-strand	187-190	4	2
β-strand	195-198	4	2
β-strand	205-206	2	3
α-helix	225-228	4
α-helix	237-252	16
β-strand	261	1	4
α-helix	262-273	12
α-helix	276-277	2
α-helix	278-284	7
α-helix	286-288	3
α-helix	297-300	4
α-helix	301-304	4
α-helix	311-320	10
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-344	7
α-helix	354-356	3
α-helix	364-367	4
α-helix	371-373	3
α-helix	374-377	4

Chain B: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	38-44	7	5
β-strand	52-64	13	5
β-strand	69-75	7	5
β-strand	81-88	8	5
α-helix	89	1
β-strand	90	1	6
β-strand	93	1	6
α-helix	96-103	8
β-strand	109	1	7
β-strand	112-120	9	5
β-strand	125-133	9	5
β-strand	137-138	2	7
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-173	19
β-strand	177-178	2	8
α-helix	184-186	3
β-strand	187-190	4	7
β-strand	195-198	4	7
β-strand	205-206	2	8
β-strand	219	1	4
α-helix	225-228	4
α-helix	237-252	16
α-helix	262-273	12
α-helix	276-277	2
α-helix	278-284	7
α-helix	286-288	3
α-helix	297-300	4
α-helix	301-304	4
α-helix	311-320	10
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-344	7
α-helix	354-357	4
α-helix	364-367	4
α-helix	371-373	3
α-helix	374-377	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen synthase kinase-3 beta	A, B	protein	359	Homo sapiens	P49841 (AlphaFold model)
BiS-8	C, D	protein	15	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9X2Y_1 Glycogen synthase kinase-3 beta (chains A, B)
GPKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAI
KKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVAR
HYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSA
KQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVD
QLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYT
PTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR

Sequence of entity 2 (C, D), FASTA

>9X2Y_2 BiS-8 (chains C, D)
YNIEENFRFFASRYC

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	2

Water and common crystallization additives (PG4, CL) are not listed.

Primary citation

Discovery of Supra-Bivalent GSK3 beta Inhibitory Peptides Containing an ATP-Mimetic Amino Acid. Haslbock, S., Vinogradov, A.A., Okada, C. et al. J Am Chem Soc (2026) 148:368-378. DOI 10.1021/jacs.5c13788 · PubMed

Other PDB entries of the same protein (UniProt P49841 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X2V 1.39 Å, GSK3beta complexed with BiS-3
1O6L 1.6 Å, Crystal structure of an activated Akt/protein kinase B (PKB-PIF chimera) ternary complex…
9X2Q 1.68 Å, GSK3beta complexed with BiS-1
1O6K 1.7 Å, Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
9X2X 1.79 Å, GSK3beta complexed with BiS-5
1J1B 1.8 Å, Binary complex structure of human tau protein kinase I with AMPPNP
2JDO 1.8 Å, Structure of pkb-beta (AKT2) complexed with isoquinoline-5-sulfonic acid…
7SXJ 1.85 Å, BIO-2895 (BRD0705) bound GSK3beta-axin complex
3QKL 1.9 Å, Spirochromane Akt Inhibitors
9X2W 1.92 Å, GSK3beta complexed with BiS-4
2X39 1.93 Å, Structure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin-…
1Q5K 1.94 Å, crystal structure of Glycogen synthase kinase 3 in complexed with inhibitor

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