Structure

Physi-Chem Properties

Molecular Weight:  254.22
Volume:  291.68
LogP:  6.394
LogD:  4.237
LogS:  -6.129
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.577
Synthetic Accessibility Score:  2.926
Fsp3:  0.938
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:  -4.805
MDCK Permeability:  2.2032600099919364e-05
Pgp-inhibitor:  0.116
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.247
Plasma Protein Binding (PPB):  97.45374298095703%
Volume Distribution (VD):  1.289
Pgp-substrate:  1.997471570968628%

ADMET: Metabolism

CYP1A2-inhibitor:  0.771
CYP1A2-substrate:  0.192
CYP2C19-inhibitor:  0.551
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.26
CYP2C9-substrate:  0.793
CYP2D6-inhibitor:  0.169
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.38
CYP3A4-substrate:  0.09

ADMET: Excretion

Clearance (CL):  5.086
Half-life (T1/2):  0.356

ADMET: Toxicity

hERG Blockers:  0.21
Human Hepatotoxicity (H-HT):  0.085
Drug-inuced Liver Injury (DILI):  0.508
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.063
Maximum Recommended Daily Dose:  0.09
Skin Sensitization:  0.963
Carcinogencity:  0.117
Eye Corrosion:  0.912
Eye Irritation:  0.969
Respiratory Toxicity:  0.91

Download Data

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

  Natural Product: NPC94355

Natural Product ID:  NPC94355
Common Name*:   VRQBQHFFHBFLQO-LVICEBGESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VRQBQHFFHBFLQO-LVICEBGESA-N
Standard InCHI:  InChI=1S/C18H24N2O3/c1-15(11-14-21)18(23)20-13-6-5-12-19-17(22)10-9-16-7-3-2-4-8-16/h2-4,7-11,21H,5-6,12-14H2,1H3,(H,19,22)(H,20,23)/b10-9+,15-11+
SMILES:  C/C(=CCO)/C(=NCCCCN=C(/C=C/c1ccccc1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10980024
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0002810] Cinnamic acid amides

*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
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20515057]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27623 Citrus japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28052 Miriquidica leucophaea Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20222 Franseria ambrosioides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27623 Citrus japonica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18130.1 Erophaca baetica subsp. baetica Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19682 Duguetia chrysocarpa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20667 Cereus queretaroensis Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22318 Sechium edule Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7864 Pyrola media Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13294 Pinus yunnanensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18179 Leucopaxillus amarus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6578 Aglaia dasyclada Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21632 Chlorobium phaeovibrioides Species Chlorobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23171 Hygrophorus olivaceoalbus Species Hygrophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21152 Senecio asper Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23092 Ammodendron karelinii Species Fabaceae 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 NPC94355 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 NPC94355 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