Structure of PDB 3iop Chain A Binding Site BS01

Receptor Information
>3iop Chain A (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKV
PYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKI
GSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDF
GTAKVLSSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFR
AGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGY
GPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand ID8I1
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-/m1/s1
InChIKeyXNXUJUXYVTYIGP-LJQANCHMSA-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
CACTVS 3.352COc1cc2ncc3c(N)nc(cc3c2cc1OC)c4cncc(OC[C@H](N)Cc5ccccc5)c4
OpenEye OEToolkits 1.7.0COc1cc2c3cc(nc(c3cnc2cc1OC)N)c4cc(cnc4)OC[C@@H](Cc5ccccc5)N
FormulaC28 H27 N5 O3
Name2-(5-{[(2R)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine
ChEMBLCHEMBL1095294
DrugBank
ZINCZINC000044675807
PDB chain3iop Chain A Residue 1 [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]
PDB3iop 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).
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G89 E90 G91 S94 V96 A109 K111 L159 S160 Y161 A162 G165 E209 L212 T222 D223
Binding residue
(residue number reindexed from 1)		G15 E16 G17 S20 V22 A35 K37 L85 S86 Y87 A88 G91 E135 L138 T148 D149
Annotation score1
Binding affinityMOAD: ic50=17nM
PDBbind-CN: -logKd/Ki=7.77,IC50=17nM
BindingDB: IC50=17nM
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 T162
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3iop, PDBe:3iop, PDBj:3iop
PDBsum3iop
PubMed20074837
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

[Back to BioLiP]