Structure

Physi-Chem Properties

Molecular Weight:  268.28
Volume:  326.038
LogP:  6.415
LogD:  5.608
LogS:  -5.913
# Rotatable Bonds:  12
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.423
Synthetic Accessibility Score:  3.005
Fsp3:  0.944
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:  -4.525
MDCK Permeability:  1.1508758689160459e-05
Pgp-inhibitor:  0.78
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.409
Plasma Protein Binding (PPB):  97.0211410522461%
Volume Distribution (VD):  1.448
Pgp-substrate:  2.457798719406128%

ADMET: Metabolism

CYP1A2-inhibitor:  0.371
CYP1A2-substrate:  0.198
CYP2C19-inhibitor:  0.359
CYP2C19-substrate:  0.341
CYP2C9-inhibitor:  0.477
CYP2C9-substrate:  0.961
CYP2D6-inhibitor:  0.04
CYP2D6-substrate:  0.059
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.106

ADMET: Excretion

Clearance (CL):  7.804
Half-life (T1/2):  0.159

ADMET: Toxicity

hERG Blockers:  0.07
Human Hepatotoxicity (H-HT):  0.06
Drug-inuced Liver Injury (DILI):  0.394
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.946
Carcinogencity:  0.106
Eye Corrosion:  0.991
Eye Irritation:  0.942
Respiratory Toxicity:  0.563

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

  Natural Product: NPC229676

Natural Product ID:  NPC229676
Common Name*:   WHWDWIHXSPCOKZ-IRXDYDNUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WHWDWIHXSPCOKZ-IRXDYDNUSA-N
Standard InCHI:  InChI=1S/C18H36O/c1-15(2)9-6-10-16(3)11-7-12-17(4)13-8-14-18(5)19/h15-17H,6-14H2,1-5H3/t16-,17-/m0/s1
SMILES:  CC(C)CCC[C@H](C)CCC[C@H](C)CCCC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   1810797
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO2251 Sphagneticola trilobata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22574649]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[26594776]
NPO2251 Sphagneticola trilobata Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[26946839]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[30381950]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO2251 Sphagneticola trilobata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[33306388]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30493 Common rush n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20519 Cytisus striatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20892 Glochidion wrightii Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19961 Corydalis humosa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20199 Euphorbia tortilis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20083 Perezia recurvata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22751 Gentiana flavo-maculata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22302 Murraya microphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21593 Vulpes vulpes Species Canidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21847 Lecanora vinetorum Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2251 Sphagneticola trilobata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28276 Artemisia argyi 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 NPC229676 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 NPC229676 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