Structure of PDB 2r7b Chain A Binding Site BS02

Receptor Information
>2r7b 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
GTAKVLFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAG
NEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGP
LKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand ID253
InChIInChI=1S/C19H18N4O2/c1-9-13(20)5-4-10-17-11-6-15(24-2)16(25-3)7-14(11)22-8-12(17)19(21)23-18(9)10/h4-8H,20H2,1-3H3,(H2,21,23)
InChIKeyNVINUNQBDNEMSY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cc2ncc3c(N)nc4c(C)c(N)ccc4c3c2cc1OC
OpenEye OEToolkits 1.5.0Cc1c(ccc2c1nc(c3c2c4cc(c(cc4nc3)OC)OC)N)N
ACDLabs 10.04n2c1cc(OC)c(OC)cc1c4c(c2)c(nc3c(c(N)ccc34)C)N
FormulaC19 H18 N4 O2
Name10,11-dimethoxy-4-methyldibenzo[c,f]-2,7-naphthyridine-3,6-diamine
ChEMBLCHEMBL235157
DrugBankDB06932
ZINC
PDB chain2r7b Chain A Residue 701 [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]
PDB2r7b Discovery of Dibenzo[c,f][2,7]naphthyridines as Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 Inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V96 A109 S160 Y161 A162 L212 T222
Binding residue
(residue number reindexed from 1)		V22 A35 S86 Y87 A88 L138 T148
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,IC50=0.06uM
BindingDB: IC50=60nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2r7b, PDBe:2r7b, PDBj:2r7b
PDBsum2r7b
PubMed17941624
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

[Back to BioLiP]