Structure

Physi-Chem Properties

Molecular Weight:  278.22
Volume:  326.919
LogP:  5.328
LogD:  4.251
LogS:  -4.251
# Rotatable Bonds:  13
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.348
Synthetic Accessibility Score:  2.589
Fsp3:  0.611
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.127
MDCK Permeability:  2.4259506972157396e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.04
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.666

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  100.55989837646484%
Volume Distribution (VD):  0.309
Pgp-substrate:  0.6503970623016357%

ADMET: Metabolism

CYP1A2-inhibitor:  0.132
CYP1A2-substrate:  0.171
CYP2C19-inhibitor:  0.054
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.307
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.16
CYP2D6-substrate:  0.783
CYP3A4-inhibitor:  0.108
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  2.07
Half-life (T1/2):  0.887

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.786
Drug-inuced Liver Injury (DILI):  0.005
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.932
Skin Sensitization:  0.955
Carcinogencity:  0.053
Eye Corrosion:  0.963
Eye Irritation:  0.979
Respiratory Toxicity:  0.352

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

  Natural Product: NPC121921

Natural Product ID:  NPC121921
Common Name*:   URPOYURDCLCHHB-ICUOVBAUSA-M
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  URPOYURDCLCHHB-ICUOVBAUSA-M
Standard InCHI:  InChI=1S/C18H30O2.Ca/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20;/h3-4,6-7,9-10H,2,5,8,11-17H2,1H3,(H,19,20);/q;+2/p-1/b4-3+,7-6+,10-9+;
SMILES:  CC/C=C/C/C=C/C/C=C/CCCCCCCC(=O)[O-].[Ca+2]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6365309
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000504] Lineolic acids 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
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO30707 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16724855]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9439 Ulmus pumila Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30707 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16963 Fructus leonuri n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9439 Ulmus pumila Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16963 Fructus leonuri n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30707 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9439 Ulmus pumila Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9439 Ulmus pumila Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae 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 NPC121921 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 NPC121921 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