Structure of PDB 6c8r Chain B Binding Site BS02

Receptor Information
>6c8r Chain B (length=356) Species: 4058 (Catharanthus roseus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVEAHPMKGGDDSHSYSQNSCYQKGVIDAAKAVIVEAVNEKLDLENNPIF
DPIKPFRIADFGCSTGPNTFHAMQNIVESVETKYKSLQKTPEFHVFFNDH
VNNDFNVLFRSLPPNREFFAAGVPGSFYTRVFPKNSIHFAHCSYALHWLS
KVPKEIQDKNSLAYNKGRIHYTGTEKHVVKAYFGQFQRDFEGFLKARAQE
IVVGGLMVIQIPGLPSGEVLFSRTGAGLLHFLLGTSLMELVNKGIINEES
VDSFNLPQYHPSVEDLEMVIEMNDCFTIERVGTLPHPMKNLPFDVQRTSL
QVRAIMECILTEHFGENILDPLFEIYTKNLQENFHVFDKEIRKDADLYLV
LKRKGN
Ligand information
Ligand IDEQV
InChIInChI=1S/C16H24O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4-6,8-13,15-21H,2-3H2,1H3,(H,22,23)/t5-,6+,8-,9+,10+,11+,12-,13+,15-,16-/m0/s1
InChIKeyJNNGEAWILNVFFD-CDJYTOATSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1[C@@H](O)C[C@H]2[C@@H]1[C@@H](OC=C2C(O)=O)O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
OpenEye OEToolkits 2.0.6C[C@H]1[C@H](C[C@H]2[C@@H]1[C@@H](OC=C2C(=O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
OpenEye OEToolkits 2.0.6CC1C(CC2C1C(OC=C2C(=O)O)OC3C(C(C(C(O3)CO)O)O)O)O
CACTVS 3.385C[CH]1[CH](O)C[CH]2[CH]1[CH](OC=C2C(O)=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O
ACDLabs 12.01CC1C(CC2C(=COC(C12)OC3C(C(C(C(O3)CO)O)O)O)C(=O)O)O
FormulaC16 H24 O10
NameLoganic acid;
(1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxyl ic acid
ChEMBLCHEMBL1081585
DrugBank
ZINCZINC000003978795
PDB chain6c8r Chain B Residue 402 [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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PDB6c8r Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside.
Resolution1.951 Å
Binding residue
(original residue number in PDB)		Y37 Q38 Y159 H162 W163 A241 H245 Q273 Q316 I320
Binding residue
(residue number reindexed from 1)		Y22 Q23 Y144 H147 W148 A226 H230 Q258 Q301 I305
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.50: loganate O-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0030749 loganate O-methyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0032259 methylation
GO:0035834 indole alkaloid metabolic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6c8r, PDBe:6c8r, PDBj:6c8r
PDBsum6c8r
PubMed29399933
UniProtB2KPR3|LAMT_CATRO Loganic acid O-methyltransferase (Gene Name=LAMT)

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