Structure of PDB 3ion Chain A Binding Site BS01

Receptor Information
>3ion Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKV
PYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKI
GSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDF
GTAKVLSVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAG
NEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGP
LKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand ID8H1
InChIInChI=1S/C28H27N5O3/c1-34-26-11-22-21-10-24(33-28(30)23(21)15-32-25(22)12-27(26)35-2)18-9-20(14-31-13-18)36-16-19(29)8-17-6-4-3-5-7-17/h3-7,9-15,19H,8,16,29H2,1-2H3,(H2,30,33)/t19-/m0/s1
InChIKeyXNXUJUXYVTYIGP-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1cc2ncc3c(N)nc(cc3c2cc1OC)c4cncc(OC[CH](N)Cc5ccccc5)c4
ACDLabs 11.02n2c1cc(OC)c(OC)cc1c5c(c2)c(nc(c4cc(OCC(N)Cc3ccccc3)cnc4)c5)N
OpenEye OEToolkits 1.7.0COc1cc2c3cc(nc(c3cnc2cc1OC)N)c4cc(cnc4)OCC(Cc5ccccc5)N
OpenEye OEToolkits 1.7.0COc1cc2c3cc(nc(c3cnc2cc1OC)N)c4cc(cnc4)OC[C@H](Cc5ccccc5)N
CACTVS 3.352COc1cc2ncc3c(N)nc(cc3c2cc1OC)c4cncc(OC[C@@H](N)Cc5ccccc5)c4
FormulaC28 H27 N5 O3
Name2-(5-{[(2S)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine
ChEMBLCHEMBL1097602
DrugBank
ZINCZINC000044674961
PDB chain3ion Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ion The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1).
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G89 E90 G91 S94 A109 K111 L159 S160 A162 G165 E166 N210 L212 T222 D223
Binding residue
(residue number reindexed from 1)		G15 E16 G17 S20 A35 K37 L85 S86 A88 G91 E92 N136 L138 T148 D149
Annotation score1
Binding affinityMOAD: ic50=8nM
PDBbind-CN: -logKd/Ki=8.10,IC50=8nM
BindingDB: IC50=8nM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D131 K133 E135 N136 D149 T160
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:3ion, PDBe:3ion, PDBj:3ion
PDBsum3ion
PubMed20074837
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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