Structure

Physi-Chem Properties

Molecular Weight:  196.15
Volume:  225.779
LogP:  3.645
LogD:  2.899
LogS:  -3.225
# Rotatable Bonds:  6
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.383
Synthetic Accessibility Score:  2.467
Fsp3:  0.583
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.404
MDCK Permeability:  2.9242621167213656e-05
Pgp-inhibitor:  0.836
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.351
30% Bioavailability (F30%):  0.247

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.647
Plasma Protein Binding (PPB):  94.21236419677734%
Volume Distribution (VD):  2.46
Pgp-substrate:  6.961397171020508%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.643
CYP2C19-inhibitor:  0.913
CYP2C19-substrate:  0.8
CYP2C9-inhibitor:  0.823
CYP2C9-substrate:  0.762
CYP2D6-inhibitor:  0.33
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.277
CYP3A4-substrate:  0.283

ADMET: Excretion

Clearance (CL):  8.496
Half-life (T1/2):  0.643

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.42
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.032
Skin Sensitization:  0.947
Carcinogencity:  0.108
Eye Corrosion:  0.915
Eye Irritation:  0.971
Respiratory Toxicity:  0.092

Download Data

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

  Natural Product: NPC226527

Natural Product ID:  NPC226527
Common Name*:   ZPKNTCZTABQJPS-PKNBQFBNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZPKNTCZTABQJPS-PKNBQFBNSA-N
Standard InCHI:  InChI=1S/C12H20O2/c1-5-14-12(13)9-11(4)8-6-7-10(2)3/h7,9H,5-6,8H2,1-4H3/b11-9+
SMILES:  CCOC(=O)/C=C(C)/CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5317247
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO7352 Acacia arabica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12441 Cymbopogon distans Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24168 Rhus coriaria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26209.1 Acer tataricum subsp. ginnala Subspecies Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7352 Acacia arabica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24168 Rhus coriaria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5271.1 Ampelopsis glandulosa var. brevipedunculata Varieties Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12441 Cymbopogon distans Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24168 Rhus coriaria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7352 Acacia arabica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12441 Cymbopogon distans Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7352 Acacia arabica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26209.1 Acer tataricum subsp. ginnala Subspecies Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24168 Rhus coriaria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5271.1 Ampelopsis glandulosa var. brevipedunculata Varieties Vitaceae 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 NPC226527 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 NPC226527 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