Structure

Physi-Chem Properties

Molecular Weight:  314.19
Volume:  341.995
LogP:  4.301
LogD:  3.528
LogS:  -4.117
# Rotatable Bonds:  0
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.76
Synthetic Accessibility Score:  5.187
Fsp3:  0.55
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.84
MDCK Permeability:  2.702878919080831e-05
Pgp-inhibitor:  0.558
Pgp-substrate:  0.023
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.081
Plasma Protein Binding (PPB):  96.24694061279297%
Volume Distribution (VD):  2.232
Pgp-substrate:  3.492173671722412%

ADMET: Metabolism

CYP1A2-inhibitor:  0.282
CYP1A2-substrate:  0.906
CYP2C19-inhibitor:  0.637
CYP2C19-substrate:  0.821
CYP2C9-inhibitor:  0.654
CYP2C9-substrate:  0.904
CYP2D6-inhibitor:  0.711
CYP2D6-substrate:  0.851
CYP3A4-inhibitor:  0.068
CYP3A4-substrate:  0.421

ADMET: Excretion

Clearance (CL):  1.766
Half-life (T1/2):  0.86

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.521
Drug-inuced Liver Injury (DILI):  0.086
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.213
Maximum Recommended Daily Dose:  0.927
Skin Sensitization:  0.925
Carcinogencity:  0.869
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC218171

Natural Product ID:  NPC218171
Common Name*:   YKYLWLYNDKXVIF-VOORUYIGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YKYLWLYNDKXVIF-VOORUYIGSA-N
Standard InCHI:  InChI=1S/C20H26O3/c1-12-5-6-14-7-8-16-18(20(14,3)4)17(23-19(16)22)11-13(2)10-15(21)9-12/h10,14,17H,1,5-9,11H2,2-4H3/b13-10+/t14-,17-/m0/s1
SMILES:  C=C1CC[C@H]2CCC3=C([C@H](C/C(=C/C(=O)C1)/C)OC3=O)C2(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[12398538]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[16933873]
NPO22004 Cystodytes solitus Species Polycitoridae Eukaryota n.a. n.a. n.a. PMID[18484775]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[19061391]
NPO24805 Thorecta reticulata Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[21513294]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19210 Quercus lusitanica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25061 Lactarius glyciosmus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11177 0ctiluca scintillans Species 0ctilucaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5278 Acacia cyperophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24616 Ottonia vahlii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5543 Persicaria tomentosa Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25205 Thymus borgiae Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3706 Hedypnois rhagadioloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24805 Thorecta reticulata Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24435 Beschorneria bracteata Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25684 Fagus dombeyi Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25606 Aster patagonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25631 Picris kamtschatica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25314 Usnea ceratina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22004 Cystodytes solitus Species Polycitoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23999 Rhipidothuria racowitzai n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25655 Pseudocyphellaria granulata Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6639 Flagelloscypha pilatii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2404 Heterophragma quadriloculare Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24482 Phyllanthus oxyphyllus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25427 Solanum vespertilio Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25516 Dahlia sherffii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25452 Crucigenia apiculata Species Scenedesmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23333 Michelia excelsa Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28702 Cyclolepis genistoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20428 Debregeasia salicifolia Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25485 Agathosma lanceolata Species Rutaceae 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 NPC218171 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 NPC218171 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