Structure of PDB 3ag9 Chain B Binding Site BS01

Receptor Information
>3ag9 Chain B (length=319) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHME
TGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNS
NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIY
RDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKG
YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSD
LKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPF
IPKIRVSINEKCGKEFSEF
Ligand information
Ligand IDA02
InChIInChI=1S/C40H70N18O9/c41-16-6-5-11-24(55-26(59)14-4-2-8-18-49-37(66)31-29(61)30(62)38(67-31)58-22-54-28-32(42)52-21-53-34(28)58)35(64)48-17-7-1-3-15-27(60)56-25(13-10-20-51-40(46)47)36(65)57-23(33(43)63)12-9-19-50-39(44)45/h21-25,29-31,38,61-62H,1-20,41H2,(H2,43,63)(H,48,64)(H,49,66)(H,55,59)(H,56,60)(H,57,65)(H2,42,52,53)(H4,44,45,50)(H4,46,47,51)/t23-,24-,25-,29+,30-,31+,38-/m1/s1
InChIKeyLIYNJKNSBUCWCZ-SAPGASOESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C(=O)NCCCCCC(=O)NC(CCCCN)C(=O)NCCCCCC(=O)NC(CCCNC(=N)N)C(=O)NC(CCCNC(=N)N)C(=O)N)O)O)N
CACTVS 3.370NCCCC[CH](NC(=O)CCCCCNC(=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(=O)NCCCCCC(=O)N[CH](CCCNC(N)=N)C(=O)N[CH](CCCNC(N)=N)C(N)=O
ACDLabs 12.01O=C(N)C(NC(=O)C(NC(=O)CCCCCNC(=O)C(NC(=O)CCCCCNC(=O)C3OC(n2cnc1c(ncnc12)N)C(O)C3O)CCCCN)CCCNC(=[N@H])N)CCCNC(=[N@H])N
OpenEye OEToolkits 1.7.0[H]/N=C(\N)/NCCC[C@H](C(=O)N)NC(=O)[C@@H](CCCN/C(=N/[H])/N)NC(=O)CCCCCNC(=O)[C@@H](CCCCN)NC(=O)CCCCCNC(=O)[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.370NCCCC[C@@H](NC(=O)CCCCCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(=O)NCCCCCC(=O)N[C@H](CCCNC(N)=N)C(=O)N[C@H](CCCNC(N)=N)C(N)=O
FormulaC40 H70 N18 O9
Name(10R,20R,23R)-10-(4-aminobutyl)-1-[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-20,23-bis(3-carbamimidamidopropyl)-1,8,11,18,21-pentaoxo-2,9,12,19,22-pentaazatetracosan-24-amide;
ARC-1012
ChEMBLCHEMBL297394
DrugBank
ZINCZINC000169360772
PDB chain3ag9 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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PDB3ag9 Diversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G52 S53 F54 G55 A70 Y122 V123 F129 D166 E170 L173 F187 E230
Binding residue
(residue number reindexed from 1)		G38 S39 F40 G41 A56 Y108 V109 F115 D152 E156 L159 F173 E216
Annotation score1
Binding affinityMOAD: Ki=9nM
PDBbind-CN: -logKd/Ki=8.05,Ki=9nM
Enzymatic activity
Catalytic site (original residue number in PDB) D166 K168 E170 N171 D184 T201
Catalytic site (residue number reindexed from 1) D152 K154 E156 N157 D170 T187
Enzyme Commision number 2.7.11.11: cAMP-dependent protein kinase.
Gene Ontology
Molecular Function
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:0005515 protein binding
GO:0005524 ATP binding
GO:0019904 protein domain specific binding
GO:0034237 protein kinase A regulatory subunit binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0001707 mesoderm formation
GO:0006468 protein phosphorylation
GO:0010737 protein kinase A signaling
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0034605 cellular response to heat
GO:1904262 negative regulation of TORC1 signaling
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005952 cAMP-dependent protein kinase complex
GO:0031594 neuromuscular junction
GO:0036126 sperm flagellum
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ag9, PDBe:3ag9, PDBj:3ag9
PDBsum3ag9
PubMed20732331
UniProtP00517|KAPCA_BOVIN cAMP-dependent protein kinase catalytic subunit alpha (Gene Name=PRKACA)

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