Structure of PDB 5lvn Chain A Binding Site BS01

Receptor Information
>5lvn Chain A (length=284) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVP
YVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG
SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFG
TAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQL
VAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRL
GCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Ligand information
Ligand IDADN
InChIInChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKeyOIRDTQYFTABQOQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
FormulaC10 H13 N5 O4
NameADENOSINE
ChEMBLCHEMBL477
DrugBankDB00640
ZINCZINC000002169830
PDB chain5lvn Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lvn Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.
Resolution1.379 Å
Binding residue
(original residue number in PDB)		G89 V96 A109 A162 E166 L212
Binding residue
(residue number reindexed from 1)		G14 V21 A34 A87 E91 L137
Annotation score3
Binding affinityMOAD: Kd=20uM
PDBbind-CN: -logKd/Ki=4.70,Kd=20uM
Enzymatic activity
Catalytic site (original residue number in PDB) D205 K207 E209 N210 D223 T245
Catalytic site (residue number reindexed from 1) D130 K132 E134 N135 D148 T170
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:5lvn, PDBe:5lvn, PDBj:5lvn
PDBsum5lvn
PubMed27693059
UniProtO15530|PDPK1_HUMAN 3-phosphoinositide-dependent protein kinase 1 (Gene Name=PDPK1)

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