Structure

Physi-Chem Properties

Molecular Weight:  224.1
Volume:  232.167
LogP:  2.751
LogD:  2.552
LogS:  -2.196
# Rotatable Bonds:  6
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.727
Synthetic Accessibility Score:  1.872
Fsp3:  0.417
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:  -4.834
MDCK Permeability:  1.6495021554874256e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.173
30% Bioavailability (F30%):  0.389

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  94.64191436767578%
Volume Distribution (VD):  0.239
Pgp-substrate:  4.8766069412231445%

ADMET: Metabolism

CYP1A2-inhibitor:  0.226
CYP1A2-substrate:  0.491
CYP2C19-inhibitor:  0.1
CYP2C19-substrate:  0.144
CYP2C9-inhibitor:  0.228
CYP2C9-substrate:  0.956
CYP2D6-inhibitor:  0.023
CYP2D6-substrate:  0.631
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.095

ADMET: Excretion

Clearance (CL):  13.285
Half-life (T1/2):  0.91

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.109
Drug-inuced Liver Injury (DILI):  0.854
AMES Toxicity:  0.215
Rat Oral Acute Toxicity:  0.167
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.378
Carcinogencity:  0.366
Eye Corrosion:  0.206
Eye Irritation:  0.82
Respiratory Toxicity:  0.092

Download Data

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

  Natural Product: NPC85040

Natural Product ID:  NPC85040
Common Name*:   TUTWQVWAOIMZDH-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  TUTWQVWAOIMZDH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H16O4/c1-2-3-6-16-10-4-5-11(13)9(7-10)8-12(14)15/h4-5,7,13H,2-3,6,8H2,1H3,(H,14,15)
SMILES:  CCCCOc1ccc(c(c1)CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15108711
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000418] Phenylacetic acids
          • [CHEMONTID:0004644] 2(hydroxyphenyl)acetic acids

*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
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[11754604]
NPO11059 Callicarpa japonica Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[12165300]
NPO19240 Ligularia cymbulifera Species Asteraceae Eukaryota Roots n.a. n.a. PMID[16643057]
NPO8080 Sarcophyton elegans Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[18004813]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota Roots Simao city, Yunnan Province, China 2007-MAY PMID[19374435]
NPO19832 Gambierdiscus toxicus Species Goniodomataceae Eukaryota n.a. n.a. n.a. PMID[21250701]
NPO9888 Lobophytum laevigatum Species Alcyoniidae Eukaryota n.a. Vietnamese n.a. PMID[21458279]
NPO9888 Lobophytum laevigatum Species Alcyoniidae Eukaryota n.a. Vietnamese soft coral n.a. PMID[21507644]
NPO11059 Callicarpa japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9222055]
NPO18599 Pangium edule Species Achariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27951 Vigna mungo Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO27951 Vigna mungo Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO27951 Vigna mungo Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO27951 Vigna mungo Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15786 Umbilicaria esculenta Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14715 Trollius chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14715 Trollius chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11059 Callicarpa japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22636 Sterculia foetida Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17749 Jackiella javanica Species Jackiellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16978 Entada phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15786 Umbilicaria esculenta Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16978 Entada phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22636 Sterculia foetida Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16978 Entada phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17222 Hesperis matronalis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19571 Oreopteris quelpaertensis Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19168 Solidago flexicaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19306 Cortinarius orellanus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14715 Trollius chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16978 Entada phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15786 Umbilicaria esculenta Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19706 Polyzonium rosalbum Species Polyzoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16316 Cylindrospermum muscicola Species 0stocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17749 Jackiella javanica Species Jackiellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19832 Gambierdiscus toxicus Species Goniodomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19010 Elephantopus hirtiflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18422 Stizolobium deeringianum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18672 Senecio adenophyllus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15119 Aphis graminum Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18839 Lilium umbellatum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12860 Clione antarctica Species Clionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18599 Pangium edule Species Achariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19086 Nematolepis phebalioides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21660 Magnolia montana Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19370 Coprosma areolata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17490 Trichophyton mentagrophytes Species Arthrodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15437 Aspergillus desertorum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14214 Sedum obtuso-lineare Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19766 Viguiera linearis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22636 Sterculia foetida Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14249 Diplodia natalensis Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18925 Artemisia rehan Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17894 Rhus vulgaris Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15481 Hypericum balearicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17350 Jatropha macrorhiza Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4499 Aglaia formosana Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11059 Callicarpa japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16776 Euphorbia amygdaloides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27951 Vigna mungo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18041 Cladrastis platycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13344 Helichrysum cephaloideum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26532 Gmelina asiatica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19631 Aphis pini Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2354 Rhizobium leguminosarum Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16132 Bryum argenteum Species Bryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19240 Ligularia cymbulifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13727 Hemionitis japonica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11083 Avrainvillea longicaulis Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18345 Phora velutina Species Phoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8080 Sarcophyton elegans Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9888 Lobophytum laevigatum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18260 Eremanthus seidelii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18163 Aulosira fertilissima Species Fortieaceae Bacteria 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 NPC85040 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 NPC85040 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