Structure

Physi-Chem Properties

Molecular Weight:  368.11
Volume:  348.769
LogP:  0.616
LogD:  -0.163
LogS:  -0.825
# Rotatable Bonds:  6
TPSA:  153.75
# H-Bond Aceptor:  9
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.267
Synthetic Accessibility Score:  3.893
Fsp3:  0.412
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.32
MDCK Permeability:  4.637252277461812e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.68
20% Bioavailability (F20%):  0.986
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.529
Plasma Protein Binding (PPB):  76.93551635742188%
Volume Distribution (VD):  1.223
Pgp-substrate:  23.852136611938477%

ADMET: Metabolism

CYP1A2-inhibitor:  0.05
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.05
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.072
CYP2C9-substrate:  0.788
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.214
CYP3A4-inhibitor:  0.172
CYP3A4-substrate:  0.095

ADMET: Excretion

Clearance (CL):  6.513
Half-life (T1/2):  0.891

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.286
Drug-inuced Liver Injury (DILI):  0.231
AMES Toxicity:  0.201
Rat Oral Acute Toxicity:  0.079
Maximum Recommended Daily Dose:  0.874
Skin Sensitization:  0.178
Carcinogencity:  0.17
Eye Corrosion:  0.003
Eye Irritation:  0.028
Respiratory Toxicity:  0.108

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  Natural Product: NPC157378

Natural Product ID:  NPC157378
Common Name*:   MZNIJRAPCCELQX-SMKXDYDZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MZNIJRAPCCELQX-SMKXDYDZSA-N
Standard InCHI:  InChI=1S/C17H20O9/c1-25-16(23)17(24)7-12(20)15(22)13(8-17)26-14(21)5-3-9-2-4-10(18)11(19)6-9/h2-6,12-13,15,18-20,22,24H,7-8H2,1H3/t12-,13-,15-,17+/m1/s1
SMILES:  COC(=O)[C@@]1(C[C@H]([C@H]([C@@H](C1)OC(=O)C=Cc1ccc(c(c1)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   487435
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001292] Cyclic alcohols and derivatives
            • [CHEMONTID:0002509] Cyclitols and derivatives
              • [CHEMONTID:0002512] Quinic acids and derivatives

*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
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota Artemisia mongolica n.a. n.a. PMID[11087599]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[11141124]
NPO3699 Acacia aulacocarpa Species Fabaceae Eukaryota n.a. leaf n.a. PMID[11735581]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15844965]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17602526]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
NPO3784 Saccharopolyspora spinosa Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. PMID[18345667]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota stem bark Kunming, Yunnan Province, China n.a. PMID[18986199]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. seed n.a. PMID[21049973]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[23701597]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[25819096]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. PMID[29035525]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26719 Tetrapanax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19948 Neolentinus lepideus Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7569 Guatteria boliviana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4823 Psiadia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8418 Anemone flaccida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5196 Eupatorium argentinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12153 Adenia globosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3853 Aspidosperma subincanum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12613 Catunaregam tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10483 Chrysanthemum sinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6729 Juniperus brevifolia Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10536 Rhabdonia verticillata Species Areschougiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1889 Panorpa japonica Species Panorpidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3784 Saccharopolyspora spinosa Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6237 Cryptocarya aschersoniana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11544 Vernonia lanuginosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10081 Othonna sedifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10798 Cis punctifer Species Ciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4823 Psiadia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7968 Artemisia kurramensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7569 Guatteria boliviana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7463 Ranzania japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9265 Jasonia candicans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3699 Acacia aulacocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9447 Tolypothrix tenuis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4698 Polymnia uvedalia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8120 Episcia cupreata Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6594 Hypericum sikokumontanum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO969 Streptomyces setonensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8654 Digitalis viridiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO40 Ostryopsis davidiana Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5633 Osyris abyssinica Species Santalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19948 Neolentinus lepideus Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO540 Anaphalis araneosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO471 Ardisia neriifolia Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8418 Anemone flaccida Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6802 Rothmannia wittii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13073 Thymus bashkiriensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7779 Impatiens edgeworthii Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5155 Peritassa compta Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO557 Bhesa nitidissima Species Centroplacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3597 Rheedia acuminata Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26719 Tetrapanax papyrifer Species Araliaceae 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 NPC157378 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 NPC157378 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