Structure

Physi-Chem Properties

Molecular Weight:  167.05
Volume:  156.105
LogP:  0.683
LogD:  0.77
LogS:  -0.55
# Rotatable Bonds:  0
TPSA:  21.06
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.525
Synthetic Accessibility Score:  3.456
Fsp3:  0.429
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:  -4.486
MDCK Permeability:  3.661999653559178e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.749
Plasma Protein Binding (PPB):  41.15498352050781%
Volume Distribution (VD):  1.206
Pgp-substrate:  57.17539978027344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.412
CYP1A2-substrate:  0.728
CYP2C19-inhibitor:  0.523
CYP2C19-substrate:  0.697
CYP2C9-inhibitor:  0.131
CYP2C9-substrate:  0.562
CYP2D6-inhibitor:  0.06
CYP2D6-substrate:  0.437
CYP3A4-inhibitor:  0.395
CYP3A4-substrate:  0.661

ADMET: Excretion

Clearance (CL):  6.055
Half-life (T1/2):  0.886

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.67
Drug-inuced Liver Injury (DILI):  0.961
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.086
Maximum Recommended Daily Dose:  0.675
Skin Sensitization:  0.93
Carcinogencity:  0.736
Eye Corrosion:  0.004
Eye Irritation:  0.022
Respiratory Toxicity:  0.383

Download Data

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

  Natural Product: NPC31504

Natural Product ID:  NPC31504
Common Name*:   OXVNSOXLMCVHBU-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OXVNSOXLMCVHBU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H9N3S/c1-9-3-2-6-4-8-5-10(6)7(9)11/h4-5H,2-3H2,1H3
SMILES:  CN1CCc2cncn2C1=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12445018
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine derivatives
          • [CHEMONTID:0001921] Pyrimidinethiones

*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
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. seed n.a. PMID[10075120]
NPO7344 Spiraea prunifolia Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[11473429]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[16499335]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[17228877]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[19615910]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[29323912]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[731398]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[731398]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. rhizome n.a. PMID[7714541]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[7760071]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. rhizome n.a. PMID[7798964]
NPO19895 Plectranthus hereroensis Species Lamiaceae Eukaryota Roots n.a. n.a. PMID[7931371]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[7964801]
NPO23356 Ascodesmis sphaerospora Species Ascodesmidaceae Eukaryota n.a. n.a. n.a. PMID[9868168]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23588 Ursinia anthemoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24280 Helianthus californicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23822 Polypodium aureum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23490 Dalbergia monetaria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9814 Lactarius fuliginosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7344 Spiraea prunifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23588 Ursinia anthemoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17492 Amomum reticulatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23356 Ascodesmis sphaerospora Species Ascodesmidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19895 Plectranthus hereroensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24396 Grosvenoria rimbachii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15572 Espeletiopsis purpurascens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23398 Caralluma russeliana Species Apocynaceae 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 NPC31504 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 NPC31504 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