Structure

Physi-Chem Properties

Molecular Weight:  252.1
Volume:  255.617
LogP:  0.998
LogD:  0.977
LogS:  -2.976
# Rotatable Bonds:  6
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.571
Synthetic Accessibility Score:  2.108
Fsp3:  0.385
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:  -4.579
MDCK Permeability:  2.2048063328838907e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.028
30% Bioavailability (F30%):  0.105

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.973
Plasma Protein Binding (PPB):  59.68474197387695%
Volume Distribution (VD):  1.051
Pgp-substrate:  23.362884521484375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.826
CYP1A2-substrate:  0.88
CYP2C19-inhibitor:  0.525
CYP2C19-substrate:  0.9
CYP2C9-inhibitor:  0.124
CYP2C9-substrate:  0.817
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.095
CYP3A4-substrate:  0.552

ADMET: Excretion

Clearance (CL):  9.789
Half-life (T1/2):  0.406

ADMET: Toxicity

hERG Blockers:  0.114
Human Hepatotoxicity (H-HT):  0.072
Drug-inuced Liver Injury (DILI):  0.824
AMES Toxicity:  0.042
Rat Oral Acute Toxicity:  0.793
Maximum Recommended Daily Dose:  0.045
Skin Sensitization:  0.346
Carcinogencity:  0.035
Eye Corrosion:  0.365
Eye Irritation:  0.945
Respiratory Toxicity:  0.964

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  Natural Product: NPC66704

Natural Product ID:  NPC66704
Common Name*:   ZYRBXTNFHYZHSK-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZYRBXTNFHYZHSK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H16O5/c1-8(14)5-10(15)13-11(17-3)6-9(16-2)7-12(13)18-4/h6-7H,5H2,1-4H3
SMILES:  CC(=O)CC(=O)c1c(cc(cc1OC)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5317271
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(98)00208-8]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23747095]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota Fruits n.a. n.a. PMID[29140705]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota Fruits n.a. n.a. PMID[31301930]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. PMID[7964790]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20851 Croton nepetaefolius Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO577 Lactifluus subvellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20851 Croton nepetaefolius Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20851 Croton nepetaefolius Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30949 Eugenia caryopyhllata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9456 Rubus sanctus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO173 Aconitum sajanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9718 Cyphelium chrysocephalum Species Caliciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2395 Siphonaria australis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15735 Galeocerdo arcticus Species Carcharhinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1456 Bersama abyssinica Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6072 Andinobates bombetes Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12409 Artemisia jacutica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5834 Pellicularia sasakii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6041 Lithocolletis coryli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4504 Cassia jahnii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO577 Lactifluus subvellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7383 Puccinia lagenophorae Species Pucciniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae 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 NPC66704 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 NPC66704 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