Structure

Physi-Chem Properties

Molecular Weight:  115.06
Volume:  112.421
LogP:  -0.57
LogD:  0.093
LogS:  0.471
# Rotatable Bonds:  1
TPSA:  38.33
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.517
Synthetic Accessibility Score:  3.447
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.301
MDCK Permeability:  1.8170145267504267e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.562
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.751
Plasma Protein Binding (PPB):  8.834848403930664%
Volume Distribution (VD):  0.928
Pgp-substrate:  86.92904663085938%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.299
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.6
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.186
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.156
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.186

ADMET: Excretion

Clearance (CL):  6.544
Half-life (T1/2):  0.744

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.381
Drug-inuced Liver Injury (DILI):  0.165
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.191
Skin Sensitization:  0.329
Carcinogencity:  0.046
Eye Corrosion:  0.014
Eye Irritation:  0.324
Respiratory Toxicity:  0.02

Download Data

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

  Natural Product: NPC24971

Natural Product ID:  NPC24971
Common Name*:   VULIHENHKGDFAB-RXMQYKEDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VULIHENHKGDFAB-RXMQYKEDSA-N
Standard InCHI:  InChI=1S/C5H9NO2/c1-8-5-3-2-4(7)6-5/h5H,2-3H2,1H3,(H,6,7)/t5-/m1/s1
SMILES:  CO[C@@H]1CCC(=N1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   643445
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001158] Pyrrolidones
          • [CHEMONTID:0003031] Pyrrolidine-2-ones

*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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[10978200]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087.1 Pteridium aquilinum var. latiusculum Varieties Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13087.1 Pteridium aquilinum var. latiusculum Varieties Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18120 Radix rehmanniae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1776 Attalea excelsa Species Arecaceae 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 NPC24971 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 NPC24971 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