Structure

Physi-Chem Properties

Molecular Weight:  248.19
Volume:  261.918
LogP:  2.062
LogD:  1.603
LogS:  -1.397
# 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:  -4.747
MDCK Permeability:  1.2383517059788574e-05
Pgp-inhibitor:  0.038
Pgp-substrate:  0.081
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.944
30% Bioavailability (F30%):  0.048

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.486
Plasma Protein Binding (PPB):  63.084510803222656%
Volume Distribution (VD):  1.261
Pgp-substrate:  44.03730392456055%

ADMET: Metabolism

CYP1A2-inhibitor:  0.034
CYP1A2-substrate:  0.146
CYP2C19-inhibitor:  0.052
CYP2C19-substrate:  0.872
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.772
CYP2D6-substrate:  0.741
CYP3A4-inhibitor:  0.029
CYP3A4-substrate:  0.787

ADMET: Excretion

Clearance (CL):  10.645
Half-life (T1/2):  0.678

ADMET: Toxicity

hERG Blockers:  0.059
Human Hepatotoxicity (H-HT):  0.956
Drug-inuced Liver Injury (DILI):  0.88
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.134
Maximum Recommended Daily Dose:  0.125
Skin Sensitization:  0.937
Carcinogencity:  0.606
Eye Corrosion:  0.092
Eye Irritation:  0.295
Respiratory Toxicity:  0.945

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

  Natural Product: NPC257625

Natural Product ID:  NPC257625
Common Name*:   YQMWQSMYVPLYDI-RQJABVFESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YQMWQSMYVPLYDI-RQJABVFESA-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:   11470670
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]
NPO6692 Pleurostylia opposita Species Celastraceae Eukaryota Stem bark University of Colombo Campus, Sri Lanka 2005-JUL PMID[17190474]
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]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. indopacific n.a. PMID[9917317]
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]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5725 Stephania dinklagei Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5725 Stephania dinklagei Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7537 Anabasis aphylla Species Chenopodiaceae 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]
NPO12511 Leplaea thompsonii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1051 Lathyrus cicer Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4780 Sophora griffithii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2502 Lupinus mexicanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21982 Erechtites hieraciifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3877 Chaenorhinum minus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16529 Plagiodera versicolora Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5725 Stephania dinklagei Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3866 Pistia stratiotes Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2915 Carya pecan Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21102 Thalictrum wangii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6692 Pleurostylia opposita Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1990 Cirsium eriophorum 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 NPC257625 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 NPC257625 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