Structure

Physi-Chem Properties

Molecular Weight:  314.08
Volume:  308.569
LogP:  3.483
LogD:  2.547
LogS:  -3.642
# Rotatable Bonds:  2
TPSA:  100.13
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.672
Synthetic Accessibility Score:  2.481
Fsp3:  0.118
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:  -4.982
MDCK Permeability:  1.1163026101712603e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.038
20% Bioavailability (F20%):  0.871
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  94.96683502197266%
Volume Distribution (VD):  0.618
Pgp-substrate:  7.869246482849121%

ADMET: Metabolism

CYP1A2-inhibitor:  0.965
CYP1A2-substrate:  0.939
CYP2C19-inhibitor:  0.295
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.686
CYP2C9-substrate:  0.848
CYP2D6-inhibitor:  0.591
CYP2D6-substrate:  0.82
CYP3A4-inhibitor:  0.517
CYP3A4-substrate:  0.147

ADMET: Excretion

Clearance (CL):  6.712
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.1
Human Hepatotoxicity (H-HT):  0.066
Drug-inuced Liver Injury (DILI):  0.695
AMES Toxicity:  0.336
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.896
Skin Sensitization:  0.939
Carcinogencity:  0.042
Eye Corrosion:  0.008
Eye Irritation:  0.916
Respiratory Toxicity:  0.365

Download Data

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

  Natural Product: NPC240336

Natural Product ID:  NPC240336
Common Name*:   UWOCAPHKEVQLDY-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UWOCAPHKEVQLDY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H14O6/c1-8-3-9(4-15(22-2)17(8)21)13-7-12(20)16-11(19)5-10(18)6-14(16)23-13/h3-7,18-19,21H,1-2H3
SMILES:  Cc1cc(cc(c1O)OC)c1cc(=O)c2c(cc(cc2o1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
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
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11599360]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[12081149]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12232319]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. aerial part n.a. PMID[1442064]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[15635251]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20000780]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. seed n.a. PMID[21381697]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. root n.a. PMID[22051934]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22208890]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[24660446]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota aerial parts herbal garden of Chungbuk National University, Cheongju, Korea 2012-Oct PMID[24963714]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[501363]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[7320737]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. aerial part n.a. Database[Article]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31185 Phragmites communis Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21939 Phyllostachys nigra Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31185 Phragmites communis Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19755 Artemisia anomala Species Asteraceae 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 NPC240336 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 NPC240336 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