Structure

Physi-Chem Properties

Molecular Weight:  169.15
Volume:  184.19
LogP:  1.062
LogD:  0.975
LogS:  -0.693
# Rotatable Bonds:  1
TPSA:  23.47
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.638
Synthetic Accessibility Score:  2.902
Fsp3:  1.0
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:  -4.522
MDCK Permeability:  1.106569470721297e-05
Pgp-inhibitor:  0.044
Pgp-substrate:  0.304
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.312
30% Bioavailability (F30%):  0.019

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.607
Plasma Protein Binding (PPB):  13.066988945007324%
Volume Distribution (VD):  1.284
Pgp-substrate:  83.87946319580078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.793
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.04
CYP2D6-inhibitor:  0.833
CYP2D6-substrate:  0.859
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.356

ADMET: Excretion

Clearance (CL):  12.023
Half-life (T1/2):  0.522

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.257
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.102
Maximum Recommended Daily Dose:  0.092
Skin Sensitization:  0.918
Carcinogencity:  0.598
Eye Corrosion:  0.803
Eye Irritation:  0.893
Respiratory Toxicity:  0.945

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC25694

Natural Product ID:  NPC25694
Common Name*:   HDVAWXXJVMJBAR-YHMJZVADSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HDVAWXXJVMJBAR-YHMJZVADSA-N
Standard InCHI:  InChI=1S/C10H19NO/c12-8-9-4-3-7-11-6-2-1-5-10(9)11/h9-10,12H,1-8H2/t9-,10?/m1/s1
SMILES:  C1CCN2CCC[C@H](CO)C2C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6432467
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002721] Lupinine-type 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
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. DOI[10.1246/bcsj.30.618]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[21043460]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. fruit n.a. PMID[23132311]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. PMID[27466882]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Fruits n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7414 Elephantopus scaber Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7414 Elephantopus scaber Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7414 Elephantopus scaber Species Asteraceae 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]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7414 Elephantopus scaber Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7537 Anabasis aphylla Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18853 Alstonia scholaris Species Apocynaceae 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 NPC25694 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 NPC25694 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