Structure

Physi-Chem Properties

Molecular Weight:  152.12
Volume:  170.557
LogP:  2.421
LogD:  2.356
LogS:  -2.063
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.521
Synthetic Accessibility Score:  4.468
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.694
MDCK Permeability:  2.336060060770251e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.387
Plasma Protein Binding (PPB):  78.5429916381836%
Volume Distribution (VD):  0.995
Pgp-substrate:  39.75653839111328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.057
CYP1A2-substrate:  0.907
CYP2C19-inhibitor:  0.503
CYP2C19-substrate:  0.925
CYP2C9-inhibitor:  0.086
CYP2C9-substrate:  0.748
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.497
CYP3A4-inhibitor:  0.098
CYP3A4-substrate:  0.425

ADMET: Excretion

Clearance (CL):  9.646
Half-life (T1/2):  0.725

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.246
Drug-inuced Liver Injury (DILI):  0.151
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.443
Maximum Recommended Daily Dose:  0.612
Skin Sensitization:  0.148
Carcinogencity:  0.413
Eye Corrosion:  0.917
Eye Irritation:  0.947
Respiratory Toxicity:  0.97

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  Natural Product: NPC136232

Natural Product ID:  NPC136232
Common Name*:   LHXDLQBQYFFVNW-PVSHWOEXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LHXDLQBQYFFVNW-PVSHWOEXSA-N
Standard InCHI:  InChI=1S/C10H16O/c1-9(2)7-4-5-10(3,6-7)8(9)11/h7H,4-6H2,1-3H3/t7-,10?/m1/s1
SMILES:  CC1(C)[C@@H]2CCC(C)(C2)C1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16213045
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001564] Bicyclic monoterpenoids

*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
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. fruit n.a. DOI[10.1007/s00217-007-0799-1]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. flower n.a. DOI[10.1016/j.foodchem.2011.01.077]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seeds n.a. n.a. PMID[15620261]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. seed n.a. PMID[17345316]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. flower bud n.a. PMID[17628872]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[19370929]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[22080044]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. flower bud n.a. PMID[7779269]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Root Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Twig n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7977 Fructus foeniculi n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7977 Fructus foeniculi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae 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]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO29010 Amomum compactum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21349 Punica granatum Species Lythraceae 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]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1918 Magnolia kobus Species Magnoliaceae 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 NPC136232 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 NPC136232 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