Structure of PDB 5yj9 Chain D Binding Site BS01

Receptor Information
>5yj9 Chain D (length=343) Species: 7070 (Tribolium castaneum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPIAKGTNGVVYSAKVKDYPFALKMMFNYDIQDNSMEILKAMYRETVPAR
MYYKHLPPHPNIVAIFSVFTMSLFLLMKRYDCNLQSFLSTAPSTRTSLLL
LAQLLEGVAHMTAHGIAHRDLKSDNLLLDTSEPESPILVISDFGCCLADK
TNGLSLPYTDYEMDKGGNEALMAPEIICQKPGTFSVLNYSKADLWAVGAI
AYEIFNCHNPFYGPSRLKNFNYKEGDLPKLPDEVPTVIQALVANLLKRNP
NKRLDPEVAANVCQLFLWAPSTWLKPGLKVPTSGEILQWLLSLTTKVLCE
KFERNWRRTYPEYLLISSFLCRAKLANVRNALHWIQENLPELD
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5yj9 Chain D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yj9 Structural insights into ubiquitin phosphorylation by PINK1.
Resolution2.53 Å
Binding residue
(original residue number in PDB)		A169 A194 K196 M294 K295 Y297 N300 D341 L344 D359
Binding residue
(residue number reindexed from 1)		A4 A22 K24 M77 K78 Y80 N83 D124 L127 D142
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein 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:5yj9, PDBe:5yj9, PDBj:5yj9
PDBsum5yj9
PubMed29991771
UniProtD6WMX4|PINK1_TRICA Serine/threonine-protein kinase Pink1, mitochondrial (Gene Name=Pink1)

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