Structure of PDB 2jds Chain A Binding Site BS02

Receptor Information
>2jds Chain A (length=337) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHM
ETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDN
SNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLI
YRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSK
GYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSS
DLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAP
FIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Ligand information
Ligand IDL20
InChIInChI=1S/C24H23N5O/c1-15-22-10-16(6-7-24(22)29-28-15)17-9-20(13-26-11-17)30-14-19(25)8-18-12-27-23-5-3-2-4-21(18)23/h2-7,9-13,19,27H,8,14,25H2,1H3,(H,28,29)/t19-/m0/s1
InChIKeyYWTBGJGMTBHQTM-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1n[nH]c2ccc(cc12)c3cncc(OC[CH](N)Cc4c[nH]c5ccccc45)c3
OpenEye OEToolkits 1.5.0Cc1c2cc(ccc2[nH]n1)c3cc(cnc3)OC[C@H](Cc4c[nH]c5c4cccc5)N
CACTVS 3.341Cc1n[nH]c2ccc(cc12)c3cncc(OC[C@@H](N)Cc4c[nH]c5ccccc45)c3
OpenEye OEToolkits 1.5.0Cc1c2cc(ccc2[nH]n1)c3cc(cnc3)OCC(Cc4c[nH]c5c4cccc5)N
ACDLabs 10.04n2c(c1cc(ccc1n2)c5cc(OCC(N)Cc4c3ccccc3nc4)cnc5)C
FormulaC24 H23 N5 O
Name(2S)-1-(1H-INDOL-3-YL)-3-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE
ChEMBLCHEMBL379300
DrugBankDB08073
ZINCZINC000016052239
PDB chain2jds Chain A Residue 1351 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2jds A Structural Comparison of Inhibitor Binding to Pkb, Pka and Pka-Pkb Chimera
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G52 G55 R56 A70 K72 M120 E121 Y122 N171 L173 T183 D184 F327
Binding residue
(residue number reindexed from 1)		G39 G42 R43 A57 K59 M107 E108 Y109 N158 L160 T170 D171 F314
Annotation score1
Binding affinityMOAD: Ki=6.3nM
PDBbind-CN: -logKd/Ki=8.20,Ki=6.3nM
BindingDB: IC50=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D166 K168 E170 N171 D184 T201
Catalytic site (residue number reindexed from 1) D153 K155 E157 N158 D171 T188
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2jds, PDBe:2jds, PDBj:2jds
PDBsum2jds
PubMed17275837
UniProtP00517|KAPCA_BOVIN cAMP-dependent protein kinase catalytic subunit alpha (Gene Name=PRKACA)

[Back to BioLiP]