Structure

Physi-Chem Properties

Molecular Weight:  346.11
Volume:  325.451
LogP:  1.594
LogD:  2.177
LogS:  -4.151
# Rotatable Bonds:  2
TPSA:  72.45
# H-Bond Aceptor:  7
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.81
Synthetic Accessibility Score:  4.505
Fsp3:  0.5
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:  -4.923
MDCK Permeability:  5.6187534937635064e-05
Pgp-inhibitor:  0.984
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.088

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.734
Plasma Protein Binding (PPB):  85.90162658691406%
Volume Distribution (VD):  0.982
Pgp-substrate:  9.154203414916992%

ADMET: Metabolism

CYP1A2-inhibitor:  0.481
CYP1A2-substrate:  0.959
CYP2C19-inhibitor:  0.163
CYP2C19-substrate:  0.853
CYP2C9-inhibitor:  0.048
CYP2C9-substrate:  0.178
CYP2D6-inhibitor:  0.582
CYP2D6-substrate:  0.28
CYP3A4-inhibitor:  0.818
CYP3A4-substrate:  0.748

ADMET: Excretion

Clearance (CL):  12.8
Half-life (T1/2):  0.6

ADMET: Toxicity

hERG Blockers:  0.055
Human Hepatotoxicity (H-HT):  0.687
Drug-inuced Liver Injury (DILI):  0.541
AMES Toxicity:  0.739
Rat Oral Acute Toxicity:  0.45
Maximum Recommended Daily Dose:  0.602
Skin Sensitization:  0.335
Carcinogencity:  0.879
Eye Corrosion:  0.004
Eye Irritation:  0.04
Respiratory Toxicity:  0.102

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  Natural Product: NPC203945

Natural Product ID:  NPC203945
Common Name*:   HBIQAWIIHPPSED-MHORFTMASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HBIQAWIIHPPSED-MHORFTMASA-N
Standard InCHI:  InChI=1S/C18H18O7/c1-20-17-15-10-6-12-13(23-8-22-12)7-11(10)24-16(15)18(21-2)4-3-9(19)5-14(18)25-17/h5-7,15-17H,3-4,8H2,1-2H3/t15-,16+,17-,18-/m0/s1
SMILES:  CO[C@@H]1[C@H]2c3cc4c(cc3O[C@H]2[C@@]2(CCC(=O)C=C2O1)OC)OCO4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10831417
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000296] Benzodioxoles

*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
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10654410]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[10843587]
NPO20142 Embelia schimperi Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[11054840]
NPO18668 Asimina parviflora Species Annonaceae Eukaryota twigs n.a. n.a. PMID[1453182]
NPO19667 Hypericum styphelioides Species Hypericaceae Eukaryota leaves n.a. n.a. PMID[15165152]
NPO19667 Hypericum styphelioides Species Hypericaceae Eukaryota n.a. leaf n.a. PMID[15165152]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[15568770]
NPO18286 Lycogala epidendrum Species Enteridiidae Eukaryota n.a. n.a. n.a. PMID[15911254]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16392664]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota roots Hualien Hsien, Taiwan 2003-JUL PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[17951038]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18175961]
NPO20879 Clerodendrum bungei Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18348535]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO3152 Morella rubra Species Myricaceae Eukaryota n.a. n.a. n.a. PMID[19407970]
NPO3152 Morella rubra Species Myricaceae Eukaryota n.a. bark n.a. PMID[21553897]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24295087]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO20598 Lythrum salicaria Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[24459770]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[27575476]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[30298740]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[9868163]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. Database[Article]
NPO12056 Chondrodendron tomentosum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21375 Euphorbia nematocypha Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20598 Lythrum salicaria Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18286 Lycogala epidendrum Species Enteridiidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17334 Onopordum acanthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18668 Asimina parviflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20879 Clerodendrum bungei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3152 Morella rubra Species Myricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18286 Lycogala epidendrum Species Enteridiidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20142 Embelia schimperi Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20680 Erythrina melanacantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17334 Onopordum acanthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21375 Euphorbia nematocypha Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20489 Epilobium hirsutum Species Onagraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12056 Chondrodendron tomentosum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20598 Lythrum salicaria Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20680 Erythrina melanacantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20598 Lythrum salicaria Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21375 Euphorbia nematocypha Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17334 Onopordum acanthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18286 Lycogala epidendrum Species Enteridiidae Eukaryota n.a. n.a. n.a. Database[Title]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21170 Embelia parviflora Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28202 Helichrysum tenuifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3152 Morella rubra Species Myricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19667 Hypericum styphelioides Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20879 Clerodendrum bungei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20084 Atraphaxis spinosa Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18143 Dendronephthya griffini Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20142 Embelia schimperi Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20598 Lythrum salicaria Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16569 Gymnocalycium schickendantzii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19995 Baccharis neglecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20421 Aplophyllum alberti-regelii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20489 Epilobium hirsutum Species Onagraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11523 Erysimum leptophyllum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21375 Euphorbia nematocypha Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17849 Centaurea maculosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28072 Theonella conica Species Theonellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20680 Erythrina melanacantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21243 Siphonaria capensis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4051 Tricholoma columbetta Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21108 Eria anomala Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12313 Haplophyllum obtusifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13449 Syzygium polycephaloides Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16141 Piper regnellii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12056 Chondrodendron tomentosum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21562 Diospyros assimilis Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14241 Planchonia grandis Species Asterolecaniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17560 Pancratium sickenbergeri Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17258 Rhinella marina Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18286 Lycogala epidendrum Species Enteridiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18866 Pteridium esculentum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19810 Myxococcus stipitatus Species Myxococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9968 Shigella dysenteriae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21495 Abelia chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18668 Asimina parviflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20843 Monsonia senegalensis Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20624 Simarouba glauca Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17334 Onopordum acanthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27367 Latrunculia magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18473 Plathymenia reticulata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19036 Esenbeckia leiocarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19511 Dolabella californica Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22961 Cordia leucocephala Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22937 Vernonia fagifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21631 Faramea salicifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21038 Lemaireocereus longispinus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19912 Vellozia nanuzae Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5903 Conus mus Species Conidae 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 NPC203945 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 NPC203945 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