Structure

Physi-Chem Properties

Molecular Weight:  324.08
Volume:  299.466
LogP:  -0.602
LogD:  0.289
LogS:  -2.169
# Rotatable Bonds:  3
TPSA:  129.59
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.528
Synthetic Accessibility Score:  3.567
Fsp3:  0.4
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:  -5.437
MDCK Permeability:  0.00019479870388749987
Pgp-inhibitor:  0.001
Pgp-substrate:  0.126
Human Intestinal Absorption (HIA):  0.785
20% Bioavailability (F20%):  0.088
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.629
Plasma Protein Binding (PPB):  58.700279235839844%
Volume Distribution (VD):  0.533
Pgp-substrate:  39.1353759765625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.065
CYP1A2-substrate:  0.085
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.092
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.222
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.468
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.046

ADMET: Excretion

Clearance (CL):  2.622
Half-life (T1/2):  0.399

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.078
Drug-inuced Liver Injury (DILI):  0.845
AMES Toxicity:  0.148
Rat Oral Acute Toxicity:  0.129
Maximum Recommended Daily Dose:  0.01
Skin Sensitization:  0.048
Carcinogencity:  0.931
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.019

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  Natural Product: NPC141080

Natural Product ID:  NPC141080
Common Name*:   VPAOSFFTKWUGAD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VPAOSFFTKWUGAD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H16O8/c16-6-10-12(18)13(19)14(20)15(23-10)21-8-3-1-7-2-4-11(17)22-9(7)5-8/h1-5,10,12-16,18-20H,6H2
SMILES:  c1cc(cc2c1ccc(=O)o2)OC1C(C(C(C(CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   320361
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0001743] Coumarin glycosides

*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
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO340 Orixa japonica Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[15568765]
NPO31471 Poncirus trifoliata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[17666859]
NPO2578 Morus sp. Species Sulidae Eukaryota n.a. n.a. n.a. PMID[19072214]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19128011]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[23872723]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[24175626]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24813739]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[32996318]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22944 Saussurea superba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25008 Skimmia japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17862 Zanthoxylum planispinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29208 Dictamnus albus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31471 Poncirus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO340 Orixa japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31505 Morus sp Species Sulidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29208 Dictamnus albus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25008 Skimmia japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO340 Orixa japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2578 Morus sp. Species Sulidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22944 Saussurea superba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28997 Cortex dictamni n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17862 Zanthoxylum planispinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31471 Poncirus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO340 Orixa japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29208 Dictamnus albus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25008 Skimmia japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17862 Zanthoxylum planispinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17862 Zanthoxylum planispinum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO340 Orixa japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25008 Skimmia japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22944 Saussurea superba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29208 Dictamnus albus 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 NPC141080 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 NPC141080 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