Structure

Physi-Chem Properties

Molecular Weight:  580.47
Volume:  644.271
LogP:  8.97
LogD:  5.011
LogS:  -4.328
# Rotatable Bonds:  26
TPSA:  103.29
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.082
Synthetic Accessibility Score:  4.306
Fsp3:  0.886
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
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:  -5.231
MDCK Permeability:  1.5546931535936892e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.1
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.989
30% Bioavailability (F30%):  0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.008
Plasma Protein Binding (PPB):  96.69908905029297%
Volume Distribution (VD):  1.241
Pgp-substrate:  1.7728296518325806%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.202
CYP2C19-inhibitor:  0.061
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.055
CYP2C9-substrate:  0.975
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.145
CYP3A4-inhibitor:  0.121
CYP3A4-substrate:  0.016

ADMET: Excretion

Clearance (CL):  7.173
Half-life (T1/2):  0.063

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.1
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.03
Rat Oral Acute Toxicity:  0.042
Maximum Recommended Daily Dose:  0.461
Skin Sensitization:  0.965
Carcinogencity:  0.016
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.419

Download Data

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

  Natural Product: NPC84695

Natural Product ID:  NPC84695
Common Name*:   WIRFHQRSPGKCFP-LSDHHAIUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WIRFHQRSPGKCFP-LSDHHAIUSA-N
Standard InCHI:  InChI=1S/C15H24O4/c1-6-15(5,17)8-7-14(19-18)12(4)10-13(16)9-11(2)3/h6,9,14,17-18H,1,4,7-8,10H2,2-3,5H3/t14-,15+/m0/s1
SMILES:  C=C[C@](C)(CC[C@@H](C(=C)CC(=O)C=C(C)C)OO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
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
NPO20112 Syncephalastrum racemosum Species Syncephalastraceae Eukaryota n.a. n.a. n.a. PMID[18558746]
NPO13906 Ficus mucuso Species Moraceae Eukaryota figs Tongolo-Yaound, in the Central Region of Cameroon 2008-JUN PMID[21619045]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. fruit n.a. PMID[21619045]
NPO17503 Conospermum incurvum Species n.a. n.a. n.a. n.a. n.a. PMID[7853001]
NPO12730 Heracleum maximum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18782.1 Pulsatilla cernua var. koreana Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17763 Lobularia elongata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7765 Quercus spicata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20662 Epinephelus drummondhayi Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20112 Syncephalastrum racemosum Species Syncephalastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21673 Lupinus caudatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21540 Naucleopsis stipularis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13003 Sogatella furcifera Species Delphacidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19749 Carpolobia glabrescens Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18782.1 Pulsatilla cernua var. koreana Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17503 Conospermum incurvum Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20469 Acer caesium Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21134 Thaumetopoea pityocampa Species 0todontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3030 Chaenorhinum villosum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18806 Neodilsea yendoana Species Dumontiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12730 Heracleum maximum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21224 Rubus pinfaensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20044 Schistostephium crataegifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16895 Croton sarcopetalus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20925 Fusarium culmorum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19608 Aconitum likiangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21000 Elysia halimedae Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19874 Polygonatum glaberrimum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21419 Biscogniauxia mediterranea Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21612 Anthelia glauca Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1550 Talaromyces purpureogenus Species Trichocomaceae 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 NPC84695 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 NPC84695 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