Structure of PDB 3ubd Chain A Binding Site BS01

Receptor Information
>3ubd Chain A (length=287) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQLYA
MKVLKKATLKVRDRVDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGD
LFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEE
GHIKLTDFGLSKEKKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMF
EMLTGTLPFQGKDRKETMTMILKAKLGMPQFLSPEAQSLLRMLFKRNPAN
RLGAGPDGVEEIKRHSFFSTIDWNKLYRREIHPPFKP
Ligand information
Ligand IDSL0
InChIInChI=1S/C25H24O12/c1-10-21(34-11(2)26)24(35-12(3)27)20(32)25(33-10)37-23-19(31)18-16(30)8-15(29)9-17(18)36-22(23)13-4-6-14(28)7-5-13/h4-10,20-21,24-25,28-30,32H,1-3H3/t10-,20+,21-,24-,25-/m0/s1
InChIKeySXOZSDJHGMAEGZ-IGKKHSBFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[CH]1O[CH](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4ccc(O)cc4)[CH](O)[CH](OC(C)=O)[CH]1OC(C)=O
OpenEye OEToolkits 1.7.2CC1C(C(C(C(O1)OC2=C(Oc3cc(cc(c3C2=O)O)O)c4ccc(cc4)O)O)OC(=O)C)OC(=O)C
CACTVS 3.370C[C@@H]1O[C@@H](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4ccc(O)cc4)[C@H](O)[C@H](OC(C)=O)[C@H]1OC(C)=O
ACDLabs 12.01O=C2C(OC1OC(C(OC(=O)C)C(OC(=O)C)C1O)C)=C(Oc3cc(O)cc(O)c23)c4ccc(O)cc4
FormulaC25 H24 O12
Name5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside;
SL 0101-1
ChEMBLCHEMBL240954
DrugBank
ZINCZINC000028875874
PDB chain3ubd Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ubd Insights into the Inhibition of the p90 Ribosomal S6 Kinase (RSK) by the Flavonol Glycoside SL0101 from the 1.5 A Crystal Structure of the N-Terminal Domain of RSK2 with Bound Inhibitor.
Resolution1.53 Å
Binding residue
(original residue number in PDB)		I50 F79 K100 V131 L147 D148 E197 L200
Binding residue
(residue number reindexed from 1)		I2 F31 K52 V77 L93 D94 E143 L146
Annotation score1
Binding affinityMOAD: Kd=2.9uM
PDBbind-CN: -logKd/Ki=5.54,Kd=2.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D193 K195 E197 N198 D211 T231
Catalytic site (residue number reindexed from 1) D139 K141 E143 N144 D157 T172
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:3ubd, PDBe:3ubd, PDBj:3ubd
PDBsum3ubd
PubMed22846040
UniProtP18654|KS6A3_MOUSE Ribosomal protein S6 kinase alpha-3 (Gene Name=Rps6ka3)

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