6Y9S: GSK-3b

Crystal structure of GSK-3b in complex with the imidazo[1,5-a]pyridine-3-carboxamide inhibitor 16. Determined by X-ray diffraction at 2.03 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,853
Mol. weight: 80.73 kDa
Ligands: OHK
Released: 20 May 2020

Explore 6Y9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y9S contains 51 α-helices and 24 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: 26 helices, 12 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	81-89	9	1
α-helix	94-95	2
α-helix	96-102	7
β-strand	109	1	2
β-strand	112-118	7	1
β-strand	126-133	8	1
β-strand	137-138	2	2
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-173	19
β-strand	177-178	2	3
α-helix	184-186	3
β-strand	187-189	3	2
β-strand	196-198	3	2
β-strand	205-206	2	3
α-helix	220-222	3
α-helix	225-228	4
α-helix	237-252	16
α-helix	264-273	10
α-helix	275-277	3
α-helix	278-284	7
α-helix	297-300	4
α-helix	301-304	4
α-helix	306	1
α-helix	311-318	8
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-340	3
α-helix	341-344	4
α-helix	354-356	3
α-helix	364-367	4
α-helix	371-373	3
α-helix	374-377	4
α-helix	380-382	3

Chain B: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	38-44	7	4
β-strand	52-65	14	4
β-strand	68-75	8	4
β-strand	81-88	8	4
α-helix	96-103	8
β-strand	109	1	5
β-strand	112-118	7	4
β-strand	127-133	7	4
β-strand	137-138	2	5
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-174	20
β-strand	177-178	2	6
α-helix	184-186	3
β-strand	187-190	4	5
β-strand	195-198	4	5
β-strand	205-206	2	6
α-helix	220-222	3
α-helix	225-228	4
α-helix	238-252	15
α-helix	259-260	2
α-helix	264-273	10
α-helix	275-277	3
α-helix	278-284	7
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	331-336	6
α-helix	338-340	3
α-helix	341-344	4
α-helix	355-356	2
α-helix	364-367	4
α-helix	371-373	3
α-helix	374-377	4
α-helix	380-382	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen synthase kinase-3 beta	A, B	protein	350	Homo sapiens	P49841 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Y9S_1 Glycogen synthase kinase-3 beta (chains A, B)
SKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFK
NRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLP
VIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNV
SYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLG
TPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEA
CAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI

Ligands and cofactors

ID	Name	Formula	Copies
OHK	~{N}-(oxan-4-ylmethyl)-6-(5-propan-2-yloxypyridin-3-yl)imidazo[1,5-a]pyridine-3…	C22 H26 N4 O3	2

Water and common crystallization additives (ACT) are not listed.

Primary citation

Discovery of Novel Imidazopyridine GSK-3 beta Inhibitors Supported by Computational Approaches. Buonfiglio, R., Prati, F., Bischetti, M. et al. Molecules (2020) 25. DOI 10.3390/molecules25092163 · 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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