2X39: Rac-beta serine/threonine-protein kinase

Structure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin- 4-yl)piperidine-4-carboxamide bound to PKB. Determined by X-ray diffraction at 1.93 Å resolution. Released 23 Feb 2010.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,943
Mol. weight: 41.37 kDa
Ligands: X39
Released: 23 Feb 2010

Explore 2X39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X39 contains 19 α-helices and 16 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: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	149-151	3
β-strand	152-160	9	1
β-strand	165-171	7	1
β-strand	176-184	9	1
α-helix	185-190	6
α-helix	194-205	12
β-strand	212	1	2
α-helix	213-214	2
β-strand	215-220	6	1
β-strand	224-230	7	1
β-strand	236	1	2
α-helix	237-244	8
α-helix	249-268	20
β-strand	272	1	3
α-helix	278-280	3
β-strand	281-283	3	2
β-strand	289-291	3	2
β-strand	298	1	3
β-strand	307	1	4
β-strand	311-312	2	5
α-helix	314-316	3
α-helix	319-322	4
β-strand	327	1	4
α-helix	331-345	15
α-helix	355-364	10
α-helix	365-367	3
α-helix	375-384	10
α-helix	400-404	5
α-helix	407-409	3
α-helix	414-418	5
α-helix	423-424	2
α-helix	441-444	4
β-strand	475-476	2	1

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-11	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rac-beta serine/threonine-protein kinase	A	protein	342	HOMO SAPIENS	P31751 (AlphaFold model)
Glycogen synthase kinase-3 beta	C	protein	10	HOMO SAPIENS	P49841 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2X39_1 RAC-BETA SERINE/THREONINE-PROTEIN KINASE (chains A)
GAMDPKVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTE
SRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIV
SALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATMKTFCGTPEYLAPE
VLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIRFPRTLSPEAKSL
LAGLLKKDPKQRLGGGPSDAKEVMEHRFFLSINWQDVVQKKLLPPFKPQVTSEVDTRYFD
DEFTAQSITITPPDRYDSLGLLELDQREEQEMFEDFDYIADW

Sequence of entity 2 (C), FASTA

>2X39_2 GLYCOGEN SYNTHASE KINASE-3 BETA (chains C)
GRPRTTSFAE

Ligands and cofactors

ID	Name	Formula	Copies
X39	4-amino-N-(4-chlorobenzyl)-1-(7H-PYRROLO[2,3-d]pyrimidin-4-yl)piperidine-4-carb…	C19 H21 Cl N6 O	1

Primary citation

Discovery of 4-Amino-1-(7H-Pyrrolo[2,3-D]Pyrimidin-4-Yl)Piperidine-4-Carboxamides as Selective, Orally Active Inhibitors of Protein Kinase B (Akt). Mchardy, T., Caldwell, J.J., Cheung, K.M. et al. J Med Chem (2010) 53:2239. DOI 10.1021/JM901788J · PubMed

Other PDB entries of the same protein (UniProt P31751 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1O6L 1.6 Å, Crystal structure of an activated Akt/protein kinase B (PKB-PIF chimera) ternary complex…
1O6K 1.7 Å, Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
2JDO 1.8 Å, Structure of pkb-beta (AKT2) complexed with isoquinoline-5-sulfonic acid…
3D0E 2.0 Å, Crystal structure of human Akt2 in complex with GSK690693
9C1W 2.0 Å, Structure of AKT2 with compound 3
2UW9 2.1 Å, STRUCTURE OF PKB-BETA (AKT2) COMPLEXED WITH 4-(4-chloro-phenyl)-4-(4-(1H-pyrazol-4-yl)-ph…
1GZK 2.3 Å, Molecular mechanism for the regulation of protein kinase B/Akt by hydrophobic motif…
2JDR 2.3 Å, Structure of pkb-beta (AKT2) complexed with the inhibitor a-443654
3E87 2.3 Å, Crystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors
8Q61 2.32 Å, Co-crystal structure of human AKT2 with compound 3
1GZN 2.5 Å, Structure of PKB kinase domain
3E88 2.5 Å, Crystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors

Browse structure collections

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