Structure

Physi-Chem Properties

Molecular Weight:  274.19
Volume:  321.646
LogP:  3.488
LogD:  2.957
LogS:  -3.797
# Rotatable Bonds:  10
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.365
Synthetic Accessibility Score:  3.752
Fsp3:  0.556
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:  -4.642
MDCK Permeability:  3.547574669937603e-05
Pgp-inhibitor:  0.017
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.334
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.008
Plasma Protein Binding (PPB):  100.39534759521484%
Volume Distribution (VD):  1.434
Pgp-substrate:  1.3071786165237427%

ADMET: Metabolism

CYP1A2-inhibitor:  0.796
CYP1A2-substrate:  0.182
CYP2C19-inhibitor:  0.902
CYP2C19-substrate:  0.248
CYP2C9-inhibitor:  0.822
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.302
CYP3A4-inhibitor:  0.819
CYP3A4-substrate:  0.1

ADMET: Excretion

Clearance (CL):  5.747
Half-life (T1/2):  0.848

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.142
Drug-inuced Liver Injury (DILI):  0.887
AMES Toxicity:  0.818
Rat Oral Acute Toxicity:  0.824
Maximum Recommended Daily Dose:  0.99
Skin Sensitization:  0.957
Carcinogencity:  0.278
Eye Corrosion:  0.933
Eye Irritation:  0.981
Respiratory Toxicity:  0.968

Download Data

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

  Natural Product: NPC13418

Natural Product ID:  NPC13418
Common Name*:   ODKNULFBMLGPHW-WLPBJKJWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ODKNULFBMLGPHW-WLPBJKJWSA-N
Standard InCHI:  InChI=1S/C18H26O2/c1-2-18(20)16-14-12-10-8-6-4-3-5-7-9-11-13-15-17-19/h2,4,6,18-20H,1,3,5,7-9,11,13,15,17H2/b6-4-/t18-/m1/s1
SMILES:  C=C[C@H](C#CC#CC/C=CCCCCCCCCO)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:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[20218656]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota Tubers n.a. n.a. PMID[23356207]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[9392889]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO20941 Smilax glaucochina Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26073 Dendropanax trifidus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25790 Olea paniculata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20941 Smilax glaucochina Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26263 Peniophora filamentosa Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26019 Venegasia carpesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26238 Albizia zygia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11120.2 Brassica rapa subsp. pekinensis Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25695 Oplopanax horridus Species Araliaceae 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
NPT71 Cell Line HEK293 Homo sapiens Activity > 70.0 % PMID[32129622]

☑ 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 NPC13418 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 NPC13418 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