Structure

Physi-Chem Properties

Molecular Weight:  302.12
Volume:  305.051
LogP:  2.618
LogD:  2.789
LogS:  -3.519
# Rotatable Bonds:  3
TPSA:  68.15
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.912
Synthetic Accessibility Score:  2.91
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.756
MDCK Permeability:  1.7511114492663182e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.43
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  98.50458526611328%
Volume Distribution (VD):  0.481
Pgp-substrate:  1.7906088829040527%

ADMET: Metabolism

CYP1A2-inhibitor:  0.933
CYP1A2-substrate:  0.946
CYP2C19-inhibitor:  0.821
CYP2C19-substrate:  0.702
CYP2C9-inhibitor:  0.677
CYP2C9-substrate:  0.908
CYP2D6-inhibitor:  0.659
CYP2D6-substrate:  0.915
CYP3A4-inhibitor:  0.473
CYP3A4-substrate:  0.679

ADMET: Excretion

Clearance (CL):  11.806
Half-life (T1/2):  0.741

ADMET: Toxicity

hERG Blockers:  0.073
Human Hepatotoxicity (H-HT):  0.229
Drug-inuced Liver Injury (DILI):  0.221
AMES Toxicity:  0.335
Rat Oral Acute Toxicity:  0.428
Maximum Recommended Daily Dose:  0.952
Skin Sensitization:  0.931
Carcinogencity:  0.453
Eye Corrosion:  0.003
Eye Irritation:  0.791
Respiratory Toxicity:  0.656

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  Natural Product: NPC102832

Natural Product ID:  NPC102832
Common Name*:   NQRBAPDEZYMKFL-NSHDSACASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NQRBAPDEZYMKFL-NSHDSACASA-N
Standard InCHI:  InChI=1S/C17H18O5/c1-20-14-6-5-13(16(19)17(14)21-2)11-7-10-3-4-12(18)8-15(10)22-9-11/h3-6,8,11,18-19H,7,9H2,1-2H3/t11-/m0/s1
SMILES:  COc1ccc([C@H]2Cc3ccc(cc3OC2)O)c(c1OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10380176
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002586] O-methylated isoflavonoids
          • [CHEMONTID:0002606] 4'-O-methylated isoflavonoids

*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
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. seed n.a. DOI[10.1007/s11418-005-0009-z]
NPO1086 Botrytis cinerea Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. PMID[10691704]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. root n.a. PMID[15763368]
NPO1086 Botrytis cinerea Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. PMID[16378371]
NPO1086 Botrytis cinerea Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. PMID[16643065]
NPO8025 Aaptos ciliata Species Suberitidae Eukaryota n.a. n.a. n.a. PMID[18257536]
NPO5325 Lobophytum durum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[19177635]
NPO5325 Lobophytum durum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[19433363]
NPO2765 Oxytropis falcata Species Fabaceae Eukaryota n.a. Sunan County, Gansu Province, China 2006-JUN PMID[20684529]
NPO5608 Croton gratissimus Species Euphorbiaceae Eukaryota n.a. stem n.a. PMID[22032651]
NPO5608 Croton gratissimus Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[22032651]
NPO2765 Oxytropis falcata Species Fabaceae Eukaryota whole plant Guide County, Qinghai Province, China 2008-AUG PMID[22775441]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25844502]
NPO8257 Carpha glomerata Species Cyperaceae Eukaryota n.a. n.a. n.a. PMID[30219526]
NPO1086 Botrytis cinerea Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. PMID[32705864]
NPO784 Sinapis alba Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7845 Tephrosia elata Species Geometridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6859 Eurycoma harmandiana Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3344 Bryonia alba Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1473 Xanthorhiza simplicissima Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO2131 Dactylorhiza viridis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7845 Tephrosia elata Species Geometridae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1473 Xanthorhiza simplicissima Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6859 Eurycoma harmandiana Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3344 Bryonia alba Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8790 Cyanostegia angustifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO373 Viburnum erubescens Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1473 Xanthorhiza simplicissima Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7845 Tephrosia elata Species Geometridae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9594 Lysimachia fordiana Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9091 Orthosiphon spicatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4901 Arnica mollis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2439 Diplopterygium glaucum Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2131 Dactylorhiza viridis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3151 Solanum lanceolatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6065 Brassica carinata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1473 Xanthorhiza simplicissima Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10038.1 Abies pinsapo var. marocana Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5608 Croton gratissimus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8790 Cyanostegia angustifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6859 Eurycoma harmandiana Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9737 Ampelocera edentula Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9867 Ixeris debilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2765 Oxytropis falcata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8938 Halobacillus litoralis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8257 Carpha glomerata Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3344 Bryonia alba Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5086 Alternaria macrospora Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13474 Euphrasia genargentea Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO593 Wikstroemia viridiflora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1086 Botrytis cinerea Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7845 Tephrosia elata Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7032 Marasmiellus troyanus Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10132 Schizophyllum lobatum Species Schizophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8025 Aaptos ciliata Species Suberitidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4536 Remirea maritima Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3838 Chrysosporum ovalisporum Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21472 Pterolobium hexapetalum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7418 Eucalyptus resinifera Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6807 Ranunculus asiaticus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4123 Trididemnum cyanophorum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1293 Streptomyces matensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5325 Lobophytum durum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9998 Abies excelsa Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO373 Viburnum erubescens Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5857 Achlya heterosexualis Species Saprolegniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2670 Maytenus chuchuhuasha Species Celastraceae 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 NPC102832 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 NPC102832 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