Structure

Physi-Chem Properties

Molecular Weight:  304.17
Volume:  330.67
LogP:  3.767
LogD:  2.463
LogS:  -4.006
# Rotatable Bonds:  6
TPSA:  74.6
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.787
Synthetic Accessibility Score:  2.834
Fsp3:  0.444
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:  -4.565
MDCK Permeability:  2.3767825041431934e-05
Pgp-inhibitor:  0.256
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.686
Plasma Protein Binding (PPB):  91.87081146240234%
Volume Distribution (VD):  0.79
Pgp-substrate:  5.661864757537842%

ADMET: Metabolism

CYP1A2-inhibitor:  0.661
CYP1A2-substrate:  0.188
CYP2C19-inhibitor:  0.556
CYP2C19-substrate:  0.222
CYP2C9-inhibitor:  0.788
CYP2C9-substrate:  0.896
CYP2D6-inhibitor:  0.45
CYP2D6-substrate:  0.174
CYP3A4-inhibitor:  0.176
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  4.078
Half-life (T1/2):  0.782

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.089
Drug-inuced Liver Injury (DILI):  0.36
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.047
Maximum Recommended Daily Dose:  0.197
Skin Sensitization:  0.381
Carcinogencity:  0.667
Eye Corrosion:  0.007
Eye Irritation:  0.314
Respiratory Toxicity:  0.072

Download Data

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

  Natural Product: NPC87555

Natural Product ID:  NPC87555
Common Name*:   PWVHOWFSWUREIY-VOTSOKGWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PWVHOWFSWUREIY-VOTSOKGWSA-N
Standard InCHI:  InChI=1S/C18H24O4/c1-11(2)8-16(20)15-10-14(12(3)19)9-13(17(15)21)6-7-18(4,5)22/h6-7,9-11,21-22H,8H2,1-5H3/b7-6+
SMILES:  CC(C)CC(=O)c1cc(cc(/C=C/C(C)(C)O)c1O)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5318238
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO25089 Cinchona calisaya Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[11992775]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[12828478]
NPO17936 Glycosmis arborea Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[15387647]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. root n.a. PMID[15520511]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota seeds n.a. n.a. PMID[15620254]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota seeds n.a. n.a. PMID[1624939]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17027268]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota Seeds n.a. n.a. PMID[19715321]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota Seeds n.a. n.a. PMID[19931461]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23403897]
NPO11187 Fraxinus mandshurica Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20988 Geum urbanum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18184 Macaranga triloba Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25089 Cinchona calisaya Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11187 Fraxinus mandshurica Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20988 Geum urbanum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18184 Macaranga triloba Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21583 Brenania brieyi Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20525 Swartzia leiocalycina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11187 Fraxinus mandshurica Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19116 Lachnum papyraceum Species Hyaloscyphaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12675 Prunus maximowiczii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11239 Dittrichia viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19727 Angelica edulis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20027 Streptomyces versipellis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17936 Glycosmis arborea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17421 Solanum crispum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21259 Crescentia alata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21123 Pecten opercularis Species Pectinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19421 Myristica moschata Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19941 Ophryosporus macrodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18184 Macaranga triloba Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20988 Geum urbanum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18934 Liatris mucronata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19854 Dorstenia foetida Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21186 Polyporus tumulosus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20853 Scaphander lignarius Species Scaphandridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25089 Cinchona calisaya Species Rubiaceae 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 NPC87555 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 NPC87555 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