Structure

Physi-Chem Properties

Molecular Weight:  244.07
Volume:  250.293
LogP:  1.778
LogD:  1.814
LogS:  -3.857
# Rotatable Bonds:  3
TPSA:  56.51
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.614
Synthetic Accessibility Score:  2.334
Fsp3:  0.143
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:  -4.698
MDCK Permeability:  1.6551623048144393e-05
Pgp-inhibitor:  0.128
Pgp-substrate:  0.963
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.028
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.065
Plasma Protein Binding (PPB):  85.20707702636719%
Volume Distribution (VD):  0.564
Pgp-substrate:  15.10468864440918%

ADMET: Metabolism

CYP1A2-inhibitor:  0.971
CYP1A2-substrate:  0.955
CYP2C19-inhibitor:  0.325
CYP2C19-substrate:  0.076
CYP2C9-inhibitor:  0.062
CYP2C9-substrate:  0.865
CYP2D6-inhibitor:  0.486
CYP2D6-substrate:  0.856
CYP3A4-inhibitor:  0.058
CYP3A4-substrate:  0.484

ADMET: Excretion

Clearance (CL):  9.332
Half-life (T1/2):  0.759

ADMET: Toxicity

hERG Blockers:  0.284
Human Hepatotoxicity (H-HT):  0.263
Drug-inuced Liver Injury (DILI):  0.854
AMES Toxicity:  0.24
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.768
Skin Sensitization:  0.455
Carcinogencity:  0.881
Eye Corrosion:  0.362
Eye Irritation:  0.98
Respiratory Toxicity:  0.28

Download Data

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

  Natural Product: NPC110008

Natural Product ID:  NPC110008
Common Name*:   GSVYFPMXLIFUDJ-ONEGZZNKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GSVYFPMXLIFUDJ-ONEGZZNKSA-N
Standard InCHI:  InChI=1S/C14H12O4/c1-9(15)3-4-10-7-11-5-6-14(16)18-13(11)8-12(10)17-2/h3-8H,1-2H3/b4-3+
SMILES:  CC(=O)/C=C/c1cc2ccc(=O)oc2cc1OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5321539
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives

*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
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. DOI[10.1021/jf00055a023]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[10606602]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[11539687]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[12713418]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[21080643]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. husk n.a. PMID[21574561]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. leaf n.a. PMID[21574561]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[23292602]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[29762032]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. pollen n.a. PMID[8987503]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Cob n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Husk Essent. Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Essent. Oil n.a. n.a. Database[FooDB]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13080 Gomphrena globosa Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13080 Gomphrena globosa Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5386 Citrus paradisi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13080 Gomphrena globosa Species Amaranthaceae 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 NPC110008 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 NPC110008 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