Structure

Physi-Chem Properties

Molecular Weight:  350.19
Volume:  338.501
LogP:  0.901
LogD:  1.121
LogS:  -2.191
# Rotatable Bonds:  6
TPSA:  95.84
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.693
Synthetic Accessibility Score:  4.43
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.976
MDCK Permeability:  9.556649456499144e-05
Pgp-inhibitor:  0.061
Pgp-substrate:  0.973
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.055
Plasma Protein Binding (PPB):  24.214025497436523%
Volume Distribution (VD):  0.85
Pgp-substrate:  48.51267623901367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.956
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.813
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.017
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.146
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.201

ADMET: Excretion

Clearance (CL):  2.033
Half-life (T1/2):  0.615

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.307
Drug-inuced Liver Injury (DILI):  0.635
AMES Toxicity:  0.558
Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.299
Carcinogencity:  0.057
Eye Corrosion:  0.094
Eye Irritation:  0.173
Respiratory Toxicity:  0.132

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  Natural Product: NPC161543

Natural Product ID:  NPC161543
Common Name*:   LYTHASQZLYCEJZ-ORNMZJKJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LYTHASQZLYCEJZ-ORNMZJKJSA-N
Standard InCHI:  InChI=1S/C16H30O8/c1-6-21-11-7-10(19-4)14(9(3)22-11)24-16-13(18)15(20-5)12(17)8(2)23-16/h8-18H,6-7H2,1-5H3/t8-,9-,10-,11+,12-,13-,14-,15+,16+/m1/s1
SMILES:  CCO[C@@H]1C[C@H]([C@@H]([C@@H](C)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C)O1)O)OC)O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101490302
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[10395513]
NPO7093 Oncorhynchus keta Species Salmonidae Eukaryota eggs Pacific n.a. PMID[10654418]
NPO7093 Oncorhynchus keta Species Salmonidae Eukaryota Eggs n.a. n.a. PMID[10654418]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO958 Tambja ceutae Species Polyceridae Eukaryota n.a. Azorean n.a. PMID[20227875]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. leaf n.a. PMID[9433811]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7093 Oncorhynchus keta Species Salmonidae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaves n.a. Database[FooDB]
NPO7377 Hemiphragma heterophyllum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6421 Neolitsea sericea Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6722 Anaphalis margaritacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4847 Lasianthus wallichii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27244 Dysosma pleiantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4773 Pteromys volans Species Sciuridae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7377 Hemiphragma heterophyllum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27244 Dysosma pleiantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4847 Lasianthus wallichii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6421 Neolitsea sericea Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6722 Anaphalis margaritacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6722 Anaphalis margaritacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4773 Pteromys volans Species Sciuridae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3528 Cinnamomum pedunculatum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1244 Trimusculus conica Species Trimusculidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1977 Arum montanum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6951 Dictyota spinulosa Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4050 Boronia lanceolata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO518 Mercurialis leiocarpa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3023 Achillea pratensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6421 Neolitsea sericea Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1659 Primula denticulata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1814 Euphorbia cattimandoo Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4125 Corydalis crystallina Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3456 Eucalyptus campanulata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4411 Plantago ovata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4204 Ochradenus baccatus Species Resedaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7640 Klaseopsis chinensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO798 Chloranthus holostegius Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7161 Capparis angulata Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6345 Podocarpus sellowii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9099 Carissa spinarum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4773 Pteromys volans Species Sciuridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7093 Oncorhynchus keta Species Salmonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO958 Tambja ceutae Species Polyceridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6523 Streptococcus pneumoniae Species Streptococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16714 Campanula pendula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2339 Turnera ulmifolia Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3913 Alcea nudiflora Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4350 Chlorella pyrenoidosa Species Chlorellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7377 Hemiphragma heterophyllum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6107 Acacia lemmoni Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27244 Dysosma pleiantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO586 Lomandra hastilis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5739 Rubus foliolosus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5518 Thuja dolabrata Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10450 Clerodendrum infortunatum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6722 Anaphalis margaritacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO241 Teucrium cossonii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5809 Xanthoparmelia tinctina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4847 Lasianthus wallichii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC161543 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC161543 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data