Structure

Physi-Chem Properties

Molecular Weight:  156.19
Volume:  198.812
LogP:  5.959
LogD:  4.859
LogS:  -6.001
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.479
Synthetic Accessibility Score:  1.554
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.332
MDCK Permeability:  1.222697119374061e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.649
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.613
Plasma Protein Binding (PPB):  97.48021697998047%
Volume Distribution (VD):  2.812
Pgp-substrate:  2.423945903778076%

ADMET: Metabolism

CYP1A2-inhibitor:  0.853
CYP1A2-substrate:  0.353
CYP2C19-inhibitor:  0.592
CYP2C19-substrate:  0.626
CYP2C9-inhibitor:  0.431
CYP2C9-substrate:  0.943
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.058
CYP3A4-inhibitor:  0.113
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  6.071
Half-life (T1/2):  0.166

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.17
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.798
Carcinogencity:  0.054
Eye Corrosion:  0.992
Eye Irritation:  0.979
Respiratory Toxicity:  0.419

Download Data

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

  Natural Product: NPC107015

Natural Product ID:  NPC107015
Common Name*:   CNPVJWYWYZMPDS-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CNPVJWYWYZMPDS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H24/c1-4-5-6-7-8-9-10-11(2)3/h11H,4-10H2,1-3H3
SMILES:  CCCCCCCCC(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23415
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0002500] Alkanes
          • [CHEMONTID:0004620] Branched alkanes

*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
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1078/0176-1617-00195]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[10757735]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[14735439]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. callus n.a. PMID[15715262]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17432574]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[18220354]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[22703163]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[24328283]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[24704554]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[28445039]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota Roots n.a. n.a. PMID[30024167]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32935986]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21137 Combretum indicum Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31579 Artemisia capillaries Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21137 Combretum indicum Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21137 Combretum indicum Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23548 Leonurus heterophyllus Species Lamiaceae 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 NPC107015 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 NPC107015 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