Structure

Physi-Chem Properties

Molecular Weight:  318.22
Volume:  347.268
LogP:  2.65
LogD:  2.705
LogS:  -3.338
# Rotatable Bonds:  2
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.751
Synthetic Accessibility Score:  4.566
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.159
MDCK Permeability:  2.7740925361285917e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.891
30% Bioavailability (F30%):  0.066

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.329
Plasma Protein Binding (PPB):  93.8030014038086%
Volume Distribution (VD):  0.439
Pgp-substrate:  6.147353172302246%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.304
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.607
CYP2C9-inhibitor:  0.091
CYP2C9-substrate:  0.368
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.646
CYP3A4-substrate:  0.238

ADMET: Excretion

Clearance (CL):  1.372
Half-life (T1/2):  0.746

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.079
Drug-inuced Liver Injury (DILI):  0.02
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.17
Maximum Recommended Daily Dose:  0.715
Skin Sensitization:  0.17
Carcinogencity:  0.101
Eye Corrosion:  0.293
Eye Irritation:  0.551
Respiratory Toxicity:  0.966

Download Data

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

  Natural Product: NPC269802

Natural Product ID:  NPC269802
Common Name*:   ZPZXDIXYWKXDHN-AEVHBADWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZPZXDIXYWKXDHN-AEVHBADWSA-N
Standard InCHI:  InChI=1S/C20H30O3/c1-5-18(2)10-8-14-13(12-18)6-7-15-19(14,3)11-9-16(21)20(15,4)17(22)23/h5,12,14-16,21H,1,6-11H2,2-4H3,(H,22,23)/p-1/t14-,15+,16-,18-,19+,20-/m0/s1
SMILES:  C=C[C@@]1(C)CC[C@H]2C(=C1)CC[C@@H]1[C@]2(C)CC[C@@H]([C@@]1(C)C(=O)[O-])O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101200911
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO17839 Machaerium mucronulatum Species Dolichopodidae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94598-9]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. root n.a. DOI[10.2225/vol5-issue3-fulltext-4]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. PMID[11325242]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[12088440]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[12713420]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15009205]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. PMID[16038560]
NPO1338 Arcangelisia gusanlung Species Menispermaceae Eukaryota n.a. stem n.a. PMID[21500777]
NPO9604 Amycolatopsis lurida Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. PMID[25323720]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota rhizomes Liaoning province, China 2011-SEP PMID[25927664]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[26731565]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[31419126]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15358 Entandrophragma cylindricum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5764 Ophioglossum vulgatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17831 Millettia racemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17190 Senecio erraticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13594 Hippocratea indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18242 Gleichenia glauca Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12072 Escallonia philippiana Species Escalloniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5764 Ophioglossum vulgatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17596 Ficus maxima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17068 Talaromyces wortmanni Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11603 Lathyrus macrorrhizus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11677 Lactobacillus acidophilus Species Lactobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10712 Tabebuia rosea Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21938 Coleus carnosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18377 Chaetomium retardatum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17839 Machaerium mucronulatum Species Dolichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15358 Entandrophragma cylindricum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17718 Artemisia schmidtiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18575 Ochtodes crockeri Species Rhizophyllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18173 Pyrocystis lunula Species Pyrocystaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19189 Brickellia pendula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1338 Arcangelisia gusanlung Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3050 Cladonia pseudodidyma Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17831 Millettia racemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9535 Cortinarius basirubescens Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15608 Tanacetum santolina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16829 Dunaliella acidophila Species Dunaliellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18520 Helipterum strictum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19057 Lentinellus omphalodes Species Auriscalpiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7807 Polyporus sulphureus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17275 Chamaemelum scariosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17709 Timonius kaniensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17802 Simmondsia chinensis Species Simmondsiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18061 Anacystis cyanea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12801 Aglaia meridionalis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3746 Hesperocyparis nevadensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9604 Amycolatopsis lurida Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12282 Parmelia conspersa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18792 Crotalaria lechnaultii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18847 Copaifera paupera Species Fabaceae 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 NPC269802 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 NPC269802 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