Structure

Physi-Chem Properties

Molecular Weight:  280.13
Volume:  284.289
LogP:  0.33
LogD:  0.876
LogS:  -1.613
# Rotatable Bonds:  2
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.443
Synthetic Accessibility Score:  5.074
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.727
MDCK Permeability:  7.967925193952397e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.113
Human Intestinal Absorption (HIA):  0.071
20% Bioavailability (F20%):  0.882
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.582
Plasma Protein Binding (PPB):  39.83362579345703%
Volume Distribution (VD):  0.644
Pgp-substrate:  69.89161682128906%

ADMET: Metabolism

CYP1A2-inhibitor:  0.037
CYP1A2-substrate:  0.101
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.148
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.181
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.215
CYP3A4-inhibitor:  0.047
CYP3A4-substrate:  0.186

ADMET: Excretion

Clearance (CL):  4.537
Half-life (T1/2):  0.921

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.188
Drug-inuced Liver Injury (DILI):  0.099
AMES Toxicity:  0.139
Rat Oral Acute Toxicity:  0.652
Maximum Recommended Daily Dose:  0.153
Skin Sensitization:  0.355
Carcinogencity:  0.228
Eye Corrosion:  0.005
Eye Irritation:  0.022
Respiratory Toxicity:  0.332

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

  Natural Product: NPC51248

Natural Product ID:  NPC51248
Common Name*:   HOSMFPQDFZLVEZ-GJUAHTKHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HOSMFPQDFZLVEZ-GJUAHTKHSA-N
Standard InCHI:  InChI=1S/C15H20O5/c1-9-14-12(18)5-10(7-16)3-2-4-11(8-17)6-13(14)20-15(9)19/h3,6-7,9,12-14,17-18H,2,4-5,8H2,1H3/b10-3+,11-6-/t9-,12-,13+,14+/m0/s1
SMILES:  C[C@H]1[C@@H]2[C@H](C/C(=CCC/C(=C/[C@H]2OC1=O)/CO)/C=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001771] Germacranolides 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
NPO29151 Jaborosa odonelliana Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[12027740]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16249088]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[20973550]
NPO29343 Phoebe porosa Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO28947 Dendrobium draconis Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[24844664]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy Autumn 2018 PMID[32803719]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy Spring 2019 PMID[32803719]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy PMID[32803719]
NPO29239 Anopterus glandulosus Species Escalloniaceae Eukaryota n.a. n.a. n.a. PMID[3443859]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a The rural area of Viçosa, State of Minas Gerais (MG), Brazil Adult stage PMID[35282307]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29223 Cystoseira algeriensis Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28947 Dendrobium draconis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28714 Chromolaena opadoclinia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29329 Teucrium lepicephalum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29343 Phoebe porosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29151 Jaborosa odonelliana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28782 Melodinus insulae-pinorum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29239 Anopterus glandulosus Species Escalloniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28983 Cladonia grayi Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29412 Stenocarpus sinuatus Species Proteaceae 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 NPC51248 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 NPC51248 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