Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  335.374
LogP:  7.612
LogD:  5.202
LogS:  -6.63
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.449
Synthetic Accessibility Score:  3.675
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.582
MDCK Permeability:  1.0811511856445577e-05
Pgp-inhibitor:  0.828
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.989
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.227
Plasma Protein Binding (PPB):  94.91829681396484%
Volume Distribution (VD):  6.573
Pgp-substrate:  4.614280700683594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.69
CYP1A2-substrate:  0.178
CYP2C19-inhibitor:  0.411
CYP2C19-substrate:  0.353
CYP2C9-inhibitor:  0.558
CYP2C9-substrate:  0.889
CYP2D6-inhibitor:  0.094
CYP2D6-substrate:  0.358
CYP3A4-inhibitor:  0.535
CYP3A4-substrate:  0.195

ADMET: Excretion

Clearance (CL):  13.408
Half-life (T1/2):  0.031

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.879
Drug-inuced Liver Injury (DILI):  0.081
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.007
Maximum Recommended Daily Dose:  0.236
Skin Sensitization:  0.519
Carcinogencity:  0.614
Eye Corrosion:  0.004
Eye Irritation:  0.649
Respiratory Toxicity:  0.025

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC292128

Natural Product ID:  NPC292128
Common Name*:   OIRFZVJHADZVMD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OIRFZVJHADZVMD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H32/c1-16(2)9-6-11-18(5)20-14-8-13-19(15-20)12-7-10-17(3)4/h9-10,13,20H,5-8,11-12,14-15H2,1-4H3
SMILES:  CC(=CCCC(=C)C1CCC=C(CCC=C(C)C)C1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315649
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001563] Monocyclic 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
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. stem n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. flower n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. leaf n.a. DOI[10.1007/s11418-006-0112-9]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. leaf n.a. DOI[10.1021/np50070a005]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[15930771]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[17156960]
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]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota leaves Botanical Garden of Innsbruck, Austria n.a. PMID[20100662]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. leaf n.a. PMID[21443171]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21563811]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. leaf n.a. PMID[21923134]
NPO25682 Acorus calamus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22671987]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[23373216]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25577087]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25612070]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[26422318]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota Fruits n.a. n.a. PMID[28218000]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota Radix n.a. n.a. PMID[29236488]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. PMID[6387056]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. stem n.a. Database[Article]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Plant 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]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5024 Alpinia japonica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22452 Leucanthemum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5024 Alpinia japonica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5024 Alpinia japonica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25209 Curcuma aromatica Species Zingiberaceae 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]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25618 Eriobotrya japonica Species Rosaceae 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]
NPO25209 Curcuma aromatica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5024 Alpinia japonica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25618 Eriobotrya japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22452 Leucanthemum vulgare Species Asteraceae 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 NPC292128 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 NPC292128 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