3L9M: PDB entry 3L9M

Crystal structure of PKAB3 (pka triple mutant V123A, L173M, Q181K) with compound 18. Determined by X-ray diffraction at 1.9 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,669
Mol. weight: 86.81 kDa
Ligands: L9M
Released: 19 Jan 2011

Explore 3L9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L9M contains 37 α-helices and 26 β-strands across 4 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: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	12-31	20
α-helix	40-42	3
β-strand	43-52	10	1
β-strand	55-62	8	1
β-strand	68-75	8	1
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	2
β-strand	106-111	6	1
β-strand	115-121	7	1
β-strand	126-127	2	2
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	3
α-helix	169-171	3
β-strand	172-174	3	2
β-strand	180-182	3	2
β-strand	189-190	2	3
β-strand	195	1	4
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	4
α-helix	218-233	16
α-helix	243-252	10
α-helix	263-272	10
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	311-312	2

Chain B: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	40-42	3
β-strand	43-52	10	5
β-strand	55-62	8	5
β-strand	68-75	8	5
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	6
β-strand	106-111	6	5
β-strand	115-121	7	5
β-strand	127	1	6
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	7
α-helix	169-171	3
β-strand	172-174	3	6
β-strand	180-182	3	6
β-strand	189-190	2	7
β-strand	195	1	8
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	8
α-helix	218-233	16
α-helix	243-252	10
α-helix	263-272	10
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	311-312	2
α-helix	336-338	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	18-22	5

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-21	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-dependent protein kinase catalytic subunit alpha	A, B	protein	351	Homo sapiens	P17612 (AlphaFold model)
cAMP-dependent protein kinase inhibitor alpha	C, D	protein	20	Homo sapiens	P61925 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3L9M_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A, B)
MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVML
VKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMV
MEYAPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGY
IKVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFF
ADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT
TDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (C, D), FASTA

>3L9M_2 cAMP-dependent protein kinase inhibitor alpha (chains C, D)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
L9M	(2S)-N~1~-[5-(3-methyl-1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylpheny…	C20 H22 N6 S	2

Primary citation

Azole-based inhibitors of AKT/PKB for the treatment of cancer. Zeng, Q., Allen, J.G., Bourbeau, M.P. et al. Bioorg Med Chem Lett (2010) 20:1559-1564. DOI 10.1016/j.bmcl.2010.01.067 · PubMed

Other PDB entries of the same protein (UniProt P17612 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WB8 1.55 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit),…
3OVV 1.58 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
3POO 1.6 Å, human cAMP-dependent protein kinase in complex with an inhibitor
4WB5 1.64 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit)
6QJ7 1.69 Å, Difluorophenyl diacylhydrazides: Potent inhibitors of Serum- and…
3AMA 1.75 Å, Protein kinase A sixfold mutant model of Aurora B with inhibitor JNJ-7706621
4UJ1 1.77 Å, Protein Kinase A in complex with an Inhibitor
5IZJ 1.85 Å, Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411
4UJ9 1.87 Å, Protein Kinase A in complex with an Inhibitor
3OWP 1.88 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
6FRX 1.88 Å, PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor
5BX6 1.89 Å, PKA in complex with a halogenated phthalazinone fragment compound.

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