Structure

Physi-Chem Properties

Molecular Weight:  248.19
Volume:  261.918
LogP:  2.284
LogD:  1.987
LogS:  -1.674
# Rotatable Bonds:  0
TPSA:  23.55
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.653
Synthetic Accessibility Score:  4.266
Fsp3:  0.933
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:  -4.766
MDCK Permeability:  1.0466468665981665e-05
Pgp-inhibitor:  0.041
Pgp-substrate:  0.733
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.901
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.545
Plasma Protein Binding (PPB):  36.38027572631836%
Volume Distribution (VD):  1.52
Pgp-substrate:  63.92837142944336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.028
CYP1A2-substrate:  0.11
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.87
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.097
CYP2D6-inhibitor:  0.687
CYP2D6-substrate:  0.722
CYP3A4-inhibitor:  0.033
CYP3A4-substrate:  0.765

ADMET: Excretion

Clearance (CL):  8.656
Half-life (T1/2):  0.731

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.948
Drug-inuced Liver Injury (DILI):  0.82
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.151
Maximum Recommended Daily Dose:  0.105
Skin Sensitization:  0.931
Carcinogencity:  0.604
Eye Corrosion:  0.017
Eye Irritation:  0.158
Respiratory Toxicity:  0.942

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

  Natural Product: NPC139134

Natural Product ID:  NPC139134
Common Name*:   YQMWQSMYVPLYDI-ZOBORPQBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YQMWQSMYVPLYDI-ZOBORPQBSA-N
Standard InCHI:  InChI=1S/C15H24N2O/c18-15-12-9-11(13-5-2-4-8-17(13)15)10-16-7-3-1-6-14(12)16/h11-14H,1-10H2/t11-,12+,13+,14-/m1/s1
SMILES:  C1CCN2C[C@H]3C[C@@H]([C@H]2C1)C(=O)N1CCCC[C@@H]31
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   51018055
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0001795] Sparteine, lupanine, and related alkaloids

*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
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[15043426]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23747095]
NPO3866 Pistia stratiotes Species Araceae Eukaryota n.a. n.a. n.a. PMID[24258601]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO6447 Kopsia teoi Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[9544563]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. indopacific n.a. PMID[9917317]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota 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 Leaf n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2502 Lupinus mexicanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21102 Thalictrum wangii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9464 Stevia paniculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10089 Polyalthia barnesii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11306 Crotalaria medicaginea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16529 Plagiodera versicolora Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12280 Sidastrum burrerense Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12511 Leplaea thompsonii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3866 Pistia stratiotes Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9852 Polyporus pargamenus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12164 Monnieria trifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15185 Yucca recurvifolia Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6052 Genista pichisermolliana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26187 Fritillaria stenanthera Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO621 Eria floribunda Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10968 Striga lutea Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8762 Brickellia cylindracea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21982 Erechtites hieraciifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12053 Eria alba Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7108 Rubus lambertianus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6447 Kopsia teoi Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12374 Psychotria st Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5289 Calocephalus citreus 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 NPC139134 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 NPC139134 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