Loganin

Details

• Internal ID: b7437171-36c1-4a44-adaa-49141fd89c89
• Taxonomy: Lipids and lipid-like molecules > Prenol lipids > Terpene glycosides > Iridoid O-glycosides
• IUPAC Name: methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• SMILES (Canonical): CC1C(CC2C1C(OC=C2C(=O)OC)OC3C(C(C(C(O3)CO)O)O)O)O
• SMILES (Isomeric): C[C@H]1[C@H](C[C@H]2[C@@H]1[C@@H](OC=C2C(=O)OC)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
• InChI: InChI=1S/C17H26O10/c1-6-9(19)3-7-8(15(23)24-2)5-25-16(11(6)7)27-17-14(22)13(21)12(20)10(4-18)26-17/h5-7,9-14,16-22H,3-4H2,1-2H3/t6-,7+,9-,10+,11+,12+,13-,14+,16-,17-/m0/s1
• InChI Key: AMBQHHVBBHTQBF-UOUCRYGSSA-N
• Popularity: 714 references in papers

Physical and Chemical Properties

• Molecular Formula: C₁₇H₂₆O₁₀
• Molecular Weight: 390.40 g/mol
• Exact Mass: 390.15259702 g/mol
• Topological Polar Surface Area (TPSA): 155.00 Ų
• XlogP: -1.40
• Atomic LogP (AlogP): -2.15
• H-Bond Acceptor: 10
• H-Bond Donor: 5
• Rotatable Bonds: 4

Synonyms

• 18524-94-2
• Loganoside
• 7-Hydroxy-6-desoxyverbenalin
• CHEBI:15771
• UNII-H7WJ16Q93C
• H7WJ16Q93C
• EINECS 242-398-0
• C17H26O10
• NSC 606403
• LOGANIN, (-)-
• NSC-606403
• (1S,4aS,6S,7R,7aS)-Methyl 6-hydroxy-7-methyl-1-(((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• Cyclopenta(c)pyran-4-carboxylic acid, 1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methyl-, methyl ester, (1S-(1alpha,4aalpha,6alpha,7alpha,7aalpha))-
• methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate
• (-)-Loganin
• Meliatin
• 1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta(c)pyran-4-carboxylic acid methyl ester
• 1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid methyl ester
• CYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID, 1-(.BETA.-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYL-, METHYL ESTER, (1S-(1.ALPHA.,4A.ALPHA.,6.ALPHA.,7.ALPHA.,7A.ALPHA.))-
• Cyclopenta[c]pyran-4-carboxylic acid, 1-(.beta.-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methyl-, methyl ester, [1S-(1.alpha.,4a.alpha.,6.alpha.,7.alpha.,7a.alpha.)]-
• methyl (1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta(c)pyran-4-carboxylate
• methyl (1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• Methyl (1S-(1alpha,4aalpha,6alpha,7alpha,7aalpha))-1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta(c)pyran-4-carboxylate
• Methyl [1S-(1alpha,4aalpha,6alpha,7alpha,7aalpha)]-1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylate
• Spectrum_001503
• SpecPlus_000563
• LOGANIN [MI]
• Spectrum2_001637
• Spectrum3_001875
• Spectrum4_001914
• Spectrum5_000628
• Loganin, analytical standard
• BSPBio_003350
• KBioGR_002535
• KBioSS_001983
• DivK1c_006659
• SCHEMBL307017
• SPECTRUM1504066
• SPBio_001733
• MEGxp0_000723
• 7-hydroxy-6-nu-desoxyverbenalin
• CHEMBL1081584
• ACon1_001749
• KBio1_001603
• KBio2_001983
• KBio2_004551
• KBio2_007119
• KBio3_002852
• AMBQHHVBBHTQBF-UOUCRYGSSA-N
• CYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID, 1-(.BETA.-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYL-, METHYL ESTER
• HY-N0512
• BDBM50279529
• CCG-38757
• MFCD00075645
• s3835
• AKOS022190418
• CS-5019
• LMPR0102070001
• SDCCGMLS-0066747.P001
• NCGC00178124-01
• NCGC00178124-02
• NCGC00178124-04
• AC-34479
• AS-75232
• cyclopenta(c)pyran-4-carboxylic acid, 1-(beta-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methyl-, methyl ester, (1S, 4aS, 6S, 7R, 7aS)-
• methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• C01433
• A812937
• Q-100220
• 5A5AFFBA-93AB-4635-A071-FC87B9DC023D
• Q15426222
• (1S)-1.ALPHA.-(.BETA.-D-GLUCOPYRANOSYLOXY)-1,4A.ALPHA.,5,6,7,7A.ALPHA.-HEXAHYDRO-6.ALPHA.-HYDROXY-7.ALPHA.-METHYLCYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID METHYL ESTER
• (1S)-1alpha-(beta-D-GLUCOPYRANOSYLOXY)-1,4Aalpha,5,6,7,7Aalpha-HEXAHYDRO-6alpha-HYDROXY-7alpha-METHYLCYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID METHYL ESTER
• (1S,4aS,6S,7R,7aS)-methyl 6-hydroxy-7-methyl-1-((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• (1S,4aS,6S,7R,7aS)-Methyl6-hydroxy-7-methyl-1-(((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• 6-hydroxy-7-methyl-1-[[3,4,5-trihydroxy-6-(hydroxymethyl)-2-oxanyl]oxy]-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid methyl ester
• CYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID, 1-(.BETA.-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYL-, METHYL ESTER, (1S,4AS,6S,7R,7AS)-
• CYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID, 1-(beta-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYL-, METHYL ESTER
• CYCLOPENTA(C)PYRAN-4-CARBOXYLIC ACID, 1-(beta-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYL-, METHYL ESTER, (1S,4AS,6S,7R,7AS)-
• Cyclopenta[c]pyran-4-carboxylic acid,1-(b-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methyl-, methyl ester, (1S,4aS,6S,7R,7aS)-
• methyl (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
• METHYL (1S-(1.ALPHA.,4A.ALPHA.,6.ALPHA.,7.ALPHA.,7A.ALPHA.))-1-(.BETA.-D-GLUCOPYRANOSYLOXY)-1,4A,5,6,7,7A-HEXAHYDRO-6-HYDROXY-7-METHYLCYCLOPENTA(C)PYRAN-4-CARBOXYLATE
• Methyl 6-hydroxy-7-methyl-1-((3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-1,4a,5

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	+	0.7122	71.22%
Caco-2	-	0.8351	83.51%
Blood Brain Barrier	-	0.5500	55.00%
Human oral bioavailability	-	0.8571	85.71%
Subcellular localzation	Mitochondria	0.5984	59.84%
OATP2B1 inhibitior	-	1.0000	100.00%
OATP1B1 inhibitior	-	0.5891	58.91%
OATP1B3 inhibitior	+	0.9486	94.86%
MATE1 inhibitior	-	0.9412	94.12%
OCT2 inhibitior	-	0.9500	95.00%
BSEP inhibitior	-	0.9380	93.80%
P-glycoprotein inhibitior	-	0.8839	88.39%
P-glycoprotein substrate	-	0.7613	76.13%
CYP3A4 substrate	+	0.6123	61.23%
CYP2C9 substrate	-	1.0000	100.00%
CYP2D6 substrate	-	0.8671	86.71%
CYP3A4 inhibition	-	0.9042	90.42%
CYP2C9 inhibition	-	0.9290	92.90%
CYP2C19 inhibition	-	0.9183	91.83%
CYP2D6 inhibition	-	0.8882	88.82%
CYP1A2 inhibition	-	0.8712	87.12%
CYP2C8 inhibition	-	0.6935	69.35%
CYP inhibitory promiscuity	-	0.8585	85.85%
UGT catelyzed	-	0.5000	50.00%
Carcinogenicity (binary)	-	1.0000	100.00%
Carcinogenicity (trinary)	Non-required	0.7387	73.87%
Eye corrosion	-	0.9897	98.97%
Eye irritation	-	0.9732	97.32%
Skin irritation	-	0.7277	72.77%
Skin corrosion	-	0.9494	94.94%
Ames mutagenesis	-	0.5454	54.54%
Human Ether-a-go-go-Related Gene inhibition	-	0.5561	55.61%
Micronuclear	-	0.7300	73.00%
Hepatotoxicity	-	0.7375	73.75%
skin sensitisation	-	0.8815	88.15%
Respiratory toxicity	+	0.6111	61.11%
Reproductive toxicity	+	0.9000	90.00%
Mitochondrial toxicity	+	0.5750	57.50%
Nephrotoxicity	-	0.6972	69.72%
Acute Oral Toxicity (c)	III	0.4896	48.96%
Estrogen receptor binding	+	0.5469	54.69%
Androgen receptor binding	-	0.5696	56.96%
Thyroid receptor binding	-	0.5259	52.59%
Glucocorticoid receptor binding	-	0.6330	63.30%
Aromatase binding	-	0.6069	60.69%
PPAR gamma	-	0.5457	54.57%
Honey bee toxicity	-	0.8508	85.08%
Biodegradation	-	0.6750	67.50%
Crustacea aquatic toxicity	-	0.7900	79.00%
Fish aquatic toxicity	-	0.4475	44.75%

Targets

Proven Targets:

No proven targets yet!

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL3251	P19838	Nuclear factor NF-kappa-B p105 subunit	97.84%	96.09%
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	97.16%	91.11%
CHEMBL4261	Q16665	Hypoxia-inducible factor 1 alpha	93.35%	85.14%
CHEMBL3137262	O60341	LSD1/CoREST complex	91.91%	97.09%
CHEMBL3401	O75469	Pregnane X receptor	90.59%	94.73%
CHEMBL4016	P42262	Glutamate receptor ionotropic, AMPA 2	89.85%	86.92%
CHEMBL4208	P20618	Proteasome component C5	88.35%	90.00%
CHEMBL4040	P28482	MAP kinase ERK2	87.94%	83.82%
CHEMBL3476	O15111	Inhibitor of nuclear factor kappa B kinase alpha subunit	87.38%	95.83%
CHEMBL218	P21554	Cannabinoid CB1 receptor	86.78%	96.61%
CHEMBL3060	Q9Y345	Glycine transporter 2	86.76%	99.17%
CHEMBL1806	P11388	DNA topoisomerase II alpha	84.20%	89.00%
CHEMBL2581	P07339	Cathepsin D	83.23%	98.95%
CHEMBL1075094	Q16236	Nuclear factor erythroid 2-related factor 2	81.87%	96.00%
CHEMBL253	P34972	Cannabinoid CB2 receptor	80.94%	97.25%

Plants that contains it

• Acacia aulacocarpa
• Anemonastrum flaccidum
• Arabidopsis thaliana
• Ardisia neriifolia
• Aspidosperma subincanum
• Avicennia marina subsp. marina
• Calycophyllum spruceanum
• Catharanthus roseus
• Cephalanthus occidentalis
• Cephalaria ambrosioides
• Cephalaria procera
• Cerbera manghas
• Cinchona calisaya
• Coelospermum balansanum
• Cornus officinalis
• Cryptocarya aschersoniana
• Desfontainia spinosa
• Diplopanax stachyanthus
• Dipsacus asperoides
• Dipsacus inermis
• Dipsacus laciniatus
• Eucnide bartonioides
• Eucommia ulmoides
• Eupatorium argentinum
• Fouquieria columnaris
• Garcinia madruno
• Gentiana crassicaulis
• Gentiana dahurica
• Gentiana depressa
• Gentiana macrophylla
• Gentiana pedicellata
• Gentiana pyrenaica
• Gentiana straminea
• Gentiana verna
• Guatteria ucayalina
• Guettarda platypoda
• Hydrangea macrophylla
• Jasminum nervosum
• Juniperus brevifolia
• Lippia origanoides
• Loasa tricolor
• Loasa triloba
• Lomelosia variifolia
• Lonicera angustifolia
• Lonicera caerulea
• Lonicera confusa
• Lonicera hypoglauca
• Lonicera japonica
• Lonicera macrantha
• Lonicera morrowii
• Lonicera periclymenum
• Menyanthes trifoliata
• Neonauclea sessilifolia
• Ophiorrhiza kuroiwai
• Penstemon barbatus
• Penstemon serrulatus
• Peritassa compta
• Phlomoides rotata
• Picconia excelsa
• Psiadia dentata
• Rauvolfia grandiflora
• Rauvolfia serpentina
• Scaevola floribunda
• Scaevola racemigera
• Scutellaria lateriflora
• Simira rubescens
• Simira williamsii
• Strychnos axillaris
• Strychnos lucida
• Strychnos nux-vomica
• Strychnos spinosa
• Tabernaemontana divaricata
• Timonius timon

Cross-Links

• PubChem: 87691
• NPASS: NPC35185
• LOTUS: LTS0084120
• wikiData: Q15426222