Structure

Physi-Chem Properties

Molecular Weight:  302.08
Volume:  293.909
LogP:  2.475
LogD:  2.394
LogS:  -3.774
# Rotatable Bonds:  2
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.789
Synthetic Accessibility Score:  2.89
Fsp3:  0.188
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.954
MDCK Permeability:  6.815534106863197e-06
Pgp-inhibitor:  0.005
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.327
30% Bioavailability (F30%):  0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.034
Plasma Protein Binding (PPB):  95.41712188720703%
Volume Distribution (VD):  0.717
Pgp-substrate:  5.641632080078125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.923
CYP1A2-substrate:  0.824
CYP2C19-inhibitor:  0.739
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.815
CYP2C9-substrate:  0.922
CYP2D6-inhibitor:  0.604
CYP2D6-substrate:  0.644
CYP3A4-inhibitor:  0.768
CYP3A4-substrate:  0.182

ADMET: Excretion

Clearance (CL):  14.33
Half-life (T1/2):  0.785

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.312
Drug-inuced Liver Injury (DILI):  0.943
AMES Toxicity:  0.18
Rat Oral Acute Toxicity:  0.715
Maximum Recommended Daily Dose:  0.906
Skin Sensitization:  0.903
Carcinogencity:  0.612
Eye Corrosion:  0.005
Eye Irritation:  0.933
Respiratory Toxicity:  0.835

Download Data

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

  Natural Product: NPC140925

Natural Product ID:  NPC140925
Common Name*:   FTODBIPDTXRIGS-CYBMUJFWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FTODBIPDTXRIGS-CYBMUJFWSA-N
Standard InCHI:  InChI=1S/C16H14O6/c1-21-14-4-8(2-3-10(14)18)13-7-12(20)16-11(19)5-9(17)6-15(16)22-13/h2-6,13,17-19H,7H2,1H3/t13-/m1/s1
SMILES:  COc1cc(ccc1O)[C@H]1CC(=O)c2c(cc(cc2O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12310452
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002595] 3'-O-methylated flavonoids

*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
NPO138 Daphniphyllum paxianum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[17887722]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota roots n.a. n.a. PMID[21911291]
NPO1346 Nerine bowdenii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[22312717]
NPO11877 Penicillium herquei Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26848504]
NPO8752 Xylaria cubensis Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[28802670]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[31675225]
NPO1831 Pseudodistoma arborescens Species Pseudodistomidae Eukaryota n.a. n.a. n.a. PMID[8450325]
NPO11877 Penicillium herquei Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[8609085]
NPO4969 Sesbania bispinosa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8127 Veronica arvensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11771 Strophanthus kombe Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6622 Artemisia klotzchiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14686 Justicia adhatoda Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8127 Veronica arvensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11771 Strophanthus kombe Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11771 Strophanthus kombe Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8127 Veronica arvensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25542 Streptomyces pactum Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5735 Solidago serotina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4969 Sesbania bispinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10149 Lespedeza bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14686 Justicia adhatoda Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14564 Oophaga pumilio Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6622 Artemisia klotzchiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4848 Chrysopa septempunctata Species Chrysopidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6845 Mimusops caffra Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1831 Pseudodistoma arborescens Species Pseudodistomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11823 Marine actinobacterium n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8752 Xylaria cubensis Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21255 Hymenoxys insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1697 Bitis gabonica Species Viperidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11657 Angelica lucida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2002 Drupa concatenata Species Muricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3995 Limonium sinense Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1346 Nerine bowdenii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11771 Strophanthus kombe Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11934 Castanea vesca Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9252 Adina sessilifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13472 Cotula cinerea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11877 Penicillium herquei Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO138 Daphniphyllum paxianum Species Daphniphyllaceae 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 NPC140925 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 NPC140925 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