Structure

Physi-Chem Properties

Molecular Weight:  262.12
Volume:  266.942
LogP:  1.161
LogD:  1.188
LogS:  -2.666
# Rotatable Bonds:  0
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.39
Synthetic Accessibility Score:  4.957
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.011
MDCK Permeability:  3.348416066728532e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.528
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.519
Plasma Protein Binding (PPB):  36.00878143310547%
Volume Distribution (VD):  1.068
Pgp-substrate:  58.122581481933594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.098
CYP1A2-substrate:  0.259
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.521
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.047
CYP3A4-substrate:  0.211

ADMET: Excretion

Clearance (CL):  9.738
Half-life (T1/2):  0.149

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.349
Drug-inuced Liver Injury (DILI):  0.099
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.915
Maximum Recommended Daily Dose:  0.138
Skin Sensitization:  0.303
Carcinogencity:  0.31
Eye Corrosion:  0.446
Eye Irritation:  0.439
Respiratory Toxicity:  0.982

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

  Natural Product: NPC183629

Natural Product ID:  NPC183629
Common Name*:   ZDBHCMLPJQZVAX-IHWVXMPCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZDBHCMLPJQZVAX-IHWVXMPCSA-N
Standard InCHI:  InChI=1S/C15H18O4/c1-7-4-5-15(18)8(2)6-10(16)11-9(3)14(17)19-13(11)12(7)15/h4,10-13,16,18H,2-3,5-6H2,1H3/t10-,11+,12+,13-,15+/m0/s1
SMILES:  CC1=CC[C@]2(C(=C)C[C@@H]([C@H]3C(=C)C(=O)O[C@@H]3[C@@H]12)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3082542
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:0001770] Guaianolides 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
NPO23451 Polytrichum commune Species Polytrichaceae Eukaryota n.a. n.a. n.a. PMID[19572610]
NPO17263 Mimosa diplotricha Species Fabaceae Eukaryota whole plant Taitung County, Taiwan 2009-MAY PMID[21875046]
NPO17263 Mimosa diplotricha Species Fabaceae Eukaryota n.a. aerial part n.a. PMID[21875046]
NPO17263 Mimosa diplotricha Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[27715048]
NPO23093 Blumea obliqua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[7494149]
NPO23451 Polytrichum commune Species Polytrichaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24213 Strophanthus thollonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23093 Blumea obliqua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23687 Delphinium hybridum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24326 Adenocalymma alliaceum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23451 Polytrichum commune Species Polytrichaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21955 Salvia deserta Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17263 Mimosa diplotricha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22967 Maytenus blepharodes Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20909 Astragalus amarus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18436 Agave ghiesbreghtii Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21202 Galeopsis pubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26367 Muriceopsis flavida Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24213 Strophanthus thollonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26758 Forsythia x intermedia Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18699 Baccharis articulata 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 NPC183629 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 NPC183629 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