Structure of PDB 3dne Chain A Binding Site BS02

Receptor Information
>3dne Chain A (length=338) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKH
METGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKD
NSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDL
IYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILS
KGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFS
SDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATTDWIAIYQRKVEA
PFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Ligand information
Ligand IDLL1
InChIInChI=1S/C12H9N3/c1-2-4-11-10(3-1)12(15-14-11)9-5-7-13-8-6-9/h1-8H,(H,14,15)
InChIKeyMSRXUUDVRNWSTN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04n2c(c1ccccc1n2)c3ccncc3
CACTVS 3.341[nH]1nc(c2ccncc2)c3ccccc13
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(n[nH]2)c3ccncc3
FormulaC12 H9 N3
Name3-pyridin-4-yl-1H-indazole
ChEMBLCHEMBL1234032
DrugBankDB08113
ZINCZINC000039132370
PDB chain3dne Chain A Residue 351 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dne Crystallography-independent determination of ligand binding modes
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L49 V57 A70 E121 Y122 V123 L173 T183 D184 F327
Binding residue
(residue number reindexed from 1)		L37 V45 A58 E109 Y110 V111 L161 T171 D172 F315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.22,Ki=6uM
Enzymatic activity
Catalytic site (original residue number in PDB) D166 K168 E170 N171 D184 T201
Catalytic site (residue number reindexed from 1) D154 K156 E158 N159 D172 T189
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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Cellular Component
External links
PDB RCSB:3dne, PDBe:3dne, PDBj:3dne
PDBsum3dne
PubMed18767090
UniProtP00517|KAPCA_BOVIN cAMP-dependent protein kinase catalytic subunit alpha (Gene Name=PRKACA)

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