Structure

Physi-Chem Properties

Molecular Weight:  258.05
Volume:  250.527
LogP:  2.983
LogD:  2.702
LogS:  -3.464
# Rotatable Bonds:  1
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.655
Synthetic Accessibility Score:  2.21
Fsp3:  0.071
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:  -4.85
MDCK Permeability:  1.0378469596616924e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.966
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.02
Plasma Protein Binding (PPB):  92.88523864746094%
Volume Distribution (VD):  0.803
Pgp-substrate:  9.567432403564453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.985
CYP1A2-substrate:  0.906
CYP2C19-inhibitor:  0.46
CYP2C19-substrate:  0.073
CYP2C9-inhibitor:  0.603
CYP2C9-substrate:  0.95
CYP2D6-inhibitor:  0.787
CYP2D6-substrate:  0.897
CYP3A4-inhibitor:  0.567
CYP3A4-substrate:  0.152

ADMET: Excretion

Clearance (CL):  5.407
Half-life (T1/2):  0.716

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.1
Drug-inuced Liver Injury (DILI):  0.928
AMES Toxicity:  0.663
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.888
Skin Sensitization:  0.911
Carcinogencity:  0.081
Eye Corrosion:  0.151
Eye Irritation:  0.977
Respiratory Toxicity:  0.262

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  Natural Product: NPC188167

Natural Product ID:  NPC188167
Common Name*:   XOXYHGOIRWABTC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XOXYHGOIRWABTC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H10O5/c1-18-8-5-10(16)13-12(6-8)19-11-3-2-7(15)4-9(11)14(13)17/h2-6,15-16H,1H3
SMILES:  COc1cc(c2c(c1)oc1ccc(cc1c2=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5281636
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

*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
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[10705751]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Entire plants the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Whole Plant the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. stem n.a. PMID[11908963]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[12662094]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. seed n.a. PMID[12822897]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[15104480]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. leaf n.a. PMID[15340243]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota roots n.a. n.a. PMID[16989524]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[18064621]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18064621]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota Heartwood India n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[21784631]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. rhizome n.a. PMID[22863942]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota aerial parts n.a. n.a. PMID[24042007]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24176362]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[24216090]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[24257774]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[24895551]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota seeds n.a. n.a. PMID[25466198]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[9784154]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota Tuber n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota Tubers n.a. Database[FooDB]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1087 Pterocarpus santalinus Species Fabaceae 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
NPT81 Cell Line A549 Homo sapiens IC50 = 103760.0 nM PMID[449637]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 = 87440.0 nM PMID[449637]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. PC50 > 100.0 uM PMID[449636]
NPT20985 CELL-LINE MCF7-ADR Homo sapiens IC50 = 31820.0 nM PMID[449637]

☑ 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 NPC188167 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 NPC188167 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