Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  271.747
LogP:  2.926
LogD:  3.555
LogS:  -3.333
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.689
Synthetic Accessibility Score:  4.499
Fsp3:  0.733
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:  -4.344
MDCK Permeability:  1.9610517483670264e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.069
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.844
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.965
Plasma Protein Binding (PPB):  87.96734619140625%
Volume Distribution (VD):  0.944
Pgp-substrate:  9.477974891662598%

ADMET: Metabolism

CYP1A2-inhibitor:  0.118
CYP1A2-substrate:  0.129
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.372
CYP2C9-inhibitor:  0.062
CYP2C9-substrate:  0.822
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.361
CYP3A4-inhibitor:  0.025
CYP3A4-substrate:  0.226

ADMET: Excretion

Clearance (CL):  8.433
Half-life (T1/2):  0.477

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.114
Drug-inuced Liver Injury (DILI):  0.053
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.312
Skin Sensitization:  0.296
Carcinogencity:  0.05
Eye Corrosion:  0.018
Eye Irritation:  0.263
Respiratory Toxicity:  0.616

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  Natural Product: NPC253729

Natural Product ID:  NPC253729
Common Name*:   NWWKYVMTWNUWHC-JWHNLWTMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NWWKYVMTWNUWHC-JWHNLWTMSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-10(2)13-9-8-11(3)6-5-7-12(4)14(16)15(13)17/h6,10,13-17H,4-5,7-9H2,1-3H3/b11-6+/t13-,14-,15+/m0/s1
SMILES:  CC(C)[C@@H]1CC/C(=C/CCC(=C)[C@@H]([C@@H]1O)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   100982186
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane 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
NPO2768 Berchemia floribunda Species Rhamnaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200690067]
NPO11979 Bugula neritina Species Bugulidae Eukaryota n.a. n.a. n.a. DOI[10.1021/ja00388a092]
NPO11702 Plexaurella grisea Species Plexauridae Eukaryota n.a. n.a. n.a. PMID[11325216]
NPO17377 Pittosporum viridiflorum Species Pittosporaceae Eukaryota n.a. n.a. n.a. PMID[11809069]
NPO15579 Mycale laxissima Species Mycalidae Eukaryota n.a. n.a. n.a. PMID[12932129]
NPO16634 Sinularia manaarensis Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[16933863]
NPO7664 Pseudocedrela kotschyi Species Meliaceae Eukaryota roots n.a. n.a. PMID[17253841]
NPO13975 Calanthe arisanensis Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[18640035]
NPO13975 Calanthe arisanensis Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[19193043]
NPO5018 Nervilia fordii Species Orchidaceae Eukaryota whole plant n.a. n.a. PMID[19422205]
NPO11979 Bugula neritina Species Bugulidae Eukaryota n.a. South China Sea n.a. PMID[25932671]
NPO11979 Bugula neritina Species Bugulidae Eukaryota n.a. Gulf of Aomori, Japan n.a. PMID[8691208]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. leaf n.a. PMID[8699184]
NPO11979 Bugula neritina Species Bugulidae Eukaryota n.a. n.a. n.a. PMID[8882431]
NPO16120 Swertia decora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9964 Aglaia lawii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22541 Channa argus Species Channidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15904 Chrysosplenium oppositifolium Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14127 Veratrum eschscholtzii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15691 Senecio coahuilensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13410 Mcneillia graminifolia Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22541 Channa argus Species Channidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16878 Roldana barba-johannis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27420 Venidium hirsutum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13130 0tholaena peninsularis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16223 Serratula xeranthemoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16789 Erythrina sandwicensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16553 Theonella cupola Species Theonellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2768 Berchemia floribunda Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9964 Aglaia lawii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16713 Choisya arizonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14625 Santolina rosmarinifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15341 Mucuna sloanei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14127 Veratrum eschscholtzii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8782 Arnica sachalinensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16466 Baccharis santelicis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22394 Hyacinthoides hispanica Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15579 Mycale laxissima Species Mycalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1780 Sphaeria doliolum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11702 Plexaurella grisea Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11413 Incarvillea emodi Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6899 Hepialus hecta Species Hepialidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16634 Sinularia manaarensis Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13975 Calanthe arisanensis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15194 Euphorbia balsamifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO752 Oligonychus bessardi Species Tetranychidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16313 Ochrocarpos odoratus Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5018 Nervilia fordii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1354 Myelochroa rhytidodes Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9425 Punctelia microsticta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11979 Bugula neritina Species Bugulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13773 Eriogonum nudum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13296 Pinus sitchensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17447 Agathosma betulina Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21773 Rothmannia urcelliformis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7664 Pseudocedrela kotschyi Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3742 Betula maximowicziana Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15452 Senecio othonniformis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15904 Chrysosplenium oppositifolium Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17377 Pittosporum viridiflorum Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12087 Amaioua guianensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26942 Vicoa vestita n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8298 Sphaeria biglobosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16120 Swertia decora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27425 Pseudotaxus chienii Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29072 Tritomaria quinquedentata Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5824 Hygrophila polysperma Species Acanthaceae 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 NPC253729 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 NPC253729 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