Structure of PDB 3re4 Chain A Binding Site BS01

Receptor Information
>3re4 Chain A (length=252) Species: 2234 (Archaeoglobus fulgidus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLKKIESYLDKLRIKEKDGEERKIYAEVLDGRTLKTLYKLSAKGYITAMG
GVISTGKEANVFYADGVFDGKPVAMAVKIYRIEDKMDEYLYGDERFDMRR
ISPKEKVFIWTEKEFRNLERAKEAGVSVPQPYTYMKNVLLMEFIGEDELP
APTLVELGRELKELDVEGIFNDVVENVKRLYQEAELVHADLSEYNIMYID
KVYFIDMGQAVTLRHPMAESYLERDVRNIIRFFSKYGVKADFEEMLKEVK
GE
Ligand information
Ligand IDTO1
InChIInChI=1S/C12H13N5O4/c13-1-5-2-17(11-7(5)10(14)15-4-16-11)12-9(20)8(19)6(3-18)21-12/h2,4,6,8-9,12,18-20H,3H2,(H2,14,15,16)/t6-,8-,9-,12-/m1/s1
InChIKeyXOKJUSAYZUAMGJ-WOUKDFQISA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cc(C#N)c12)[CH]3O[CH](CO)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cc(C#N)c12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
ACDLabs 12.01N#Cc2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.7.2c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)C#N
OpenEye OEToolkits 1.7.2c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)C#N
FormulaC12 H13 N5 O4
Name4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile;
TOYOCAMYCIN
ChEMBLCHEMBL99668
DrugBankDB13916
ZINCZINC000004217594
PDB chain3re4 Chain A Residue 259 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3re4 Interaction of rio1 kinase with toyocamycin reveals a conformational switch that controls oligomeric state and catalytic activity.
Resolution1.997 Å
Binding residue
(original residue number in PDB)		S56 A78 M147 F149 I150 I211
Binding residue
(residue number reindexed from 1)		S54 A76 M141 F143 I144 I205
Annotation score1
Binding affinityMOAD: Kd~40nM
PDBbind-CN: -logKd/Ki=7.40,Kd=40nM
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:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3re4, PDBe:3re4, PDBj:3re4
PDBsum3re4
PubMed22629386
UniProtO28471|RIO1_ARCFU RIO-type serine/threonine-protein kinase Rio1 (Gene Name=rio1)

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