Structure

Physi-Chem Properties

Molecular Weight:  248.14
Volume:  266.708
LogP:  2.038
LogD:  1.296
LogS:  -2.894
# Rotatable Bonds:  2
TPSA:  54.37
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.764
Synthetic Accessibility Score:  4.014
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.299
MDCK Permeability:  1.937754132086411e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.065
Plasma Protein Binding (PPB):  84.10526275634766%
Volume Distribution (VD):  0.315
Pgp-substrate:  17.020057678222656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.578
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.113
CYP2C9-inhibitor:  0.065
CYP2C9-substrate:  0.154
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.029
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  5.53
Half-life (T1/2):  0.738

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.121
Drug-inuced Liver Injury (DILI):  0.113
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.645
Maximum Recommended Daily Dose:  0.448
Skin Sensitization:  0.304
Carcinogencity:  0.661
Eye Corrosion:  0.103
Eye Irritation:  0.196
Respiratory Toxicity:  0.972

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

  Natural Product: NPC23694

Natural Product ID:  NPC23694
Common Name*:   RDGFGQJFNSCICW-ABAIWWIYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RDGFGQJFNSCICW-ABAIWWIYSA-N
Standard InCHI:  InChI=1S/C15H20O3/c1-9(14(17)18)11-4-6-15(3)7-5-13(16)10(2)12(15)8-11/h11H,1,4-8H2,2-3H3,(H,17,18)/p-1/t11-,15+/m1/s1
SMILES:  C=C([C@@H]1CC[C@@]2(C)CCC(=O)C(=C2C1)C)C(=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11054003
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids

*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
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50031a011]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18303850]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18681481]
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota bark and leaves Koh Kong Province, Cambodia 2005-DEC PMID[19053508]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19344127]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. aerial part n.a. PMID[21902175]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[26000707]
NPO14742 Uvaria cherrevensis Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[30608167]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[32880179]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19940 Delphinium brownii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11489 Primula viscosa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20984 Glycyrrhiza echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20984 Glycyrrhiza echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16644 Ormosia jamaicensis Species Limoniidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19940 Delphinium brownii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5733 Panda oleosa Species Pandaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17676 Isodon coetsa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11489 Primula viscosa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11489 Primula viscosa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11489 Primula viscosa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2839 Dovyalis abyssinica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4713 Eucalyptus cordata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21257 Lycopodium contiguum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20984 Glycyrrhiza echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO53 Nephelium mutabile Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1643 Senecio kaempferi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3212 Bipolaris sorokiniana Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5020 Jasonia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18695 Citrus limetta Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3796 Pseudomonas viridiflava Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14742 Uvaria cherrevensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5733 Panda oleosa Species Pandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20910 Cystoclonium purpureum Species Cystocloniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19045 Solenopsis geminata Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18369 Stizolophus balsamita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4861 Nectandra rubra Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21452 Robinsonia gracilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19940 Delphinium brownii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13918 Sinularia rigida Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13536 Odontoschisma denudatum Species Cephaloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8586 Phyllanthus virgatus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17676 Isodon coetsa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17664 Mucor plumbeus Species Mucoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18539 Iboza riparia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26993 Mundulea striata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16644 Ormosia jamaicensis Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13328 Bridelia balansae Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17172 Euphorbia hermentiana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17051 Bursaphelenchus xylophilus Species Aphelenchoididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17667 Varthemia iphionoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24013 Chrysomela tremula Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12645 Millettia zechiana Species Fabaceae 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
NPT81 Cell Line A549 Homo sapiens IC50 > 100000.0 nM PMID[469493]
NPT492 Cell Line Caco-2 Homo sapiens IC50 = 39000.0 nM PMID[469493]

☑ 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 NPC23694 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 NPC23694 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