Structure

Physi-Chem Properties

Molecular Weight:  260.1
Volume:  264.305
LogP:  3.279
LogD:  1.773
LogS:  -3.229
# Rotatable Bonds:  3
TPSA:  70.67
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.89
Synthetic Accessibility Score:  3.719
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.824
MDCK Permeability:  4.724963218905032e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.663
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.085

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.168
Plasma Protein Binding (PPB):  93.76146697998047%
Volume Distribution (VD):  0.377
Pgp-substrate:  6.171910285949707%

ADMET: Metabolism

CYP1A2-inhibitor:  0.073
CYP1A2-substrate:  0.487
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.16
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.022
CYP2D6-substrate:  0.131
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.099

ADMET: Excretion

Clearance (CL):  2.515
Half-life (T1/2):  0.895

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.532
Drug-inuced Liver Injury (DILI):  0.965
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.596
Maximum Recommended Daily Dose:  0.323
Skin Sensitization:  0.251
Carcinogencity:  0.885
Eye Corrosion:  0.004
Eye Irritation:  0.436
Respiratory Toxicity:  0.186

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

  Natural Product: NPC486289

Natural Product ID:  NPC486289
Common Name*:   NJYGTKDUQVRJAI-LDYMZIIASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NJYGTKDUQVRJAI-LDYMZIIASA-N
Standard InCHI:  InChI=1S/C15H16O4/c1-8(6-16)11-3-2-9-7-19-13-5-10(15(17)18)4-12(11)14(9)13/h4-5,7-8,11,16H,2-3,6H2,1H3,(H,17,18)/t8-,11-/m1/s1
SMILES:  C[C@H](CO)[C@H]1CCc2coc3cc(cc1c23)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000023] Naphthalenes
        • [CHEMONTID:0001871] Naphthalenecarboxylic acids and derivatives
          • [CHEMONTID:0002421] Naphthalenecarboxylic acids

*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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[11000018]
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[12662106]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13533 Trichoderma virens Species Hypocreaceae 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
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[31418264]
NPT1843 Organism Aeromonas hydrophila Aeromonas hydrophila MIC = 64.0 ug.mL-1 PMID[31418264]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 8.0 ug.mL-1 PMID[31418264]
NPT1726 Organism Vibrio harveyi Vibrio harveyi MIC = 16.0 ug.mL-1 PMID[31418264]
NPT565 Organism Vibrio parahaemolyticus Vibrio parahaemolyticus MIC = 32.0 ug.mL-1 PMID[31418264]
NPT2705 Organism Alternaria solani Alternaria solani MIC = 32.0 ug.mL-1 PMID[31418264]
NPT6481 Organism Bipolaris sorokiniana Bipolaris sorokiniana MIC = 8.0 ug.mL-1 PMID[31418264]
NPT1201 Organism Fusarium oxysporum f. sp. cucumerinum Fusarium oxysporum f. sp. cucumerinum MIC = 2.0 ug.mL-1 PMID[31418264]
NPT2600 Organism Fusarium solani Fusarium solani MIC = 32.0 ug.mL-1 PMID[31418264]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides MIC = 4.0 ug.mL-1 PMID[31418264]
NPT2792 Organism Penicillium digitatum Penicillium digitatum MIC = 8.0 ug.mL-1 PMID[31418264]
NPT5264 Organism Botryosphaeria berengeriana Botryosphaeria berengeriana MIC = 4.0 ug.mL-1 PMID[31418264]

☑ 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 NPC486289 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 NPC486289 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