Structure of PDB 3l9m Chain B Binding Site BS02

Receptor Information

>3l9m Chain B (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKH
KETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKD
NSNLYMVMEYAPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDL
IYRDLKPENLMIDQQGYIKVTDFGFAKRVKGRTWTLCGTPEYLAPEIILS
KGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFS
SDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEA
PFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Ligand information

Ligand ID

L9M

InChI

InChI=1S/C20H22N6S/c1-12-3-5-14(6-4-12)9-16(21)11-22-20-26-25-19(27-20)15-7-8-18-17(10-15)13(2)23-24-18/h3-8,10,16H,9,11,21H2,1-2H3,(H,22,26)(H,23,24)/t16-/m0/s1

InChIKey

RJESZRNJZYVXEA-INIZCTEOSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	Cc1ccc(cc1)CC(CNc2nnc(s2)c3ccc4c(c3)c(n[nH]4)C)N
CACTVS 3.352	Cc1ccc(C[C@H](N)CNc2sc(nn2)c3ccc4[nH]nc(C)c4c3)cc1
OpenEye OEToolkits 1.7.0	Cc1ccc(cc1)C[C@@H](CNc2nnc(s2)c3ccc4c(c3)c(n[nH]4)C)N
CACTVS 3.352	Cc1ccc(C[CH](N)CNc2sc(nn2)c3ccc4[nH]nc(C)c4c3)cc1

Formula

C20 H22 N6 S

Name

(2S)-N~1~-[5-(3-methyl-1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine

PDB chain

3l9m Chain B Residue 351 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3l9m Azole-based inhibitors of AKT/PKB for the treatment of cancer.
Resolution	1.9 Å
Binding residue (original residue number in PDB)	L49 F54 A70 K72 M120 E121 E127 E170 N171 M173 T183 D184 F327
Binding residue (residue number reindexed from 1)	L37 F42 A58 K60 M108 E109 E115 E158 N159 M161 T171 D172 F315
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	N171 D184
Catalytic site (residue number reindexed from 1)	N159 D172
Enzyme Commision number	2.7.11.11: cAMP-dependent protein kinase.

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0004672	protein kinase activity
GO:0004674	protein serine/threonine kinase activity
GO:0004679	AMP-activated protein kinase activity
GO:0004691	cAMP-dependent protein kinase activity
GO:0004712	protein serine/threonine/tyrosine kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0019901	protein kinase binding
GO:0019904	protein domain specific binding
GO:0030145	manganese ion binding
GO:0031625	ubiquitin protein ligase binding
GO:0034237	protein kinase A regulatory subunit binding
GO:0099103	channel activator activity
GO:0106310	protein serine kinase activity

	Biological Process
GO:0001707	mesoderm formation
GO:0001843	neural tube closure
GO:0002027	regulation of heart rate
GO:0003091	renal water homeostasis
GO:0006397	mRNA processing
GO:0006468	protein phosphorylation
GO:0006611	protein export from nucleus
GO:0007189	adenylate cyclase-activating G protein-coupled receptor signaling pathway
GO:0007193	adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
GO:0010737	protein kinase A signaling
GO:0010881	regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
GO:0016241	regulation of macroautophagy
GO:0016310	phosphorylation
GO:0018105	peptidyl-serine phosphorylation
GO:0019221	cytokine-mediated signaling pathway
GO:0032024	positive regulation of insulin secretion
GO:0032703	negative regulation of interleukin-2 production
GO:0034380	high-density lipoprotein particle assembly
GO:0034605	cellular response to heat
GO:0035694	mitochondrial protein catabolic process
GO:0045542	positive regulation of cholesterol biosynthetic process
GO:0045667	regulation of osteoblast differentiation
GO:0045722	positive regulation of gluconeogenesis
GO:0045879	negative regulation of smoothened signaling pathway
GO:0046827	positive regulation of protein export from nucleus
GO:0048240	sperm capacitation
GO:0050804	modulation of chemical synaptic transmission
GO:0050850	positive regulation of calcium-mediated signaling
GO:0051726	regulation of cell cycle
GO:0055117	regulation of cardiac muscle contraction
GO:0061136	regulation of proteasomal protein catabolic process
GO:0070417	cellular response to cold
GO:0070613	regulation of protein processing
GO:0071333	cellular response to glucose stimulus
GO:0071374	cellular response to parathyroid hormone stimulus
GO:0071377	cellular response to glucagon stimulus
GO:0071872	cellular response to epinephrine stimulus
GO:0086064	cell communication by electrical coupling involved in cardiac conduction
GO:0099170	postsynaptic modulation of chemical synaptic transmission
GO:1903779	regulation of cardiac conduction
GO:1904262	negative regulation of TORC1 signaling
GO:1904539	negative regulation of glycolytic process through fructose-6-phosphate
GO:1990044	protein localization to lipid droplet
GO:2000810	regulation of bicellular tight junction assembly

	Cellular Component
GO:0001669	acrosomal vesicle
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005813	centrosome
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0005930	axoneme
GO:0005952	cAMP-dependent protein kinase complex
GO:0016607	nuclear speck
GO:0031410	cytoplasmic vesicle
GO:0031514	motile cilium
GO:0031594	neuromuscular junction
GO:0034704	calcium channel complex
GO:0036126	sperm flagellum
GO:0044853	plasma membrane raft
GO:0048471	perinuclear region of cytoplasm
GO:0070062	extracellular exosome
GO:0097546	ciliary base
GO:0098794	postsynapse
GO:0098978	glutamatergic synapse

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External links

PDB	RCSB:3l9m, PDBe:3l9m, PDBj:3l9m
PDBsum	3l9m
PubMed	20137943
UniProt	P17612\|KAPCA_HUMAN cAMP-dependent protein kinase catalytic subunit alpha (Gene Name=PRKACA)

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