Structure

Physi-Chem Properties

Molecular Weight:  197.09
Volume:  183.09
LogP:  -1.735
LogD:  -1.128
LogS:  -1.721
# Rotatable Bonds:  2
TPSA:  120.25
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.308
Synthetic Accessibility Score:  3.866
Fsp3:  0.286
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:  -5.792
MDCK Permeability:  0.00011400743096601218
Pgp-inhibitor:  0.001
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.596
Plasma Protein Binding (PPB):  17.989086151123047%
Volume Distribution (VD):  1.169
Pgp-substrate:  62.483238220214844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.79
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.068
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.569
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.143

ADMET: Excretion

Clearance (CL):  1.885
Half-life (T1/2):  0.77

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.425
Drug-inuced Liver Injury (DILI):  0.299
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.693
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.142
Carcinogencity:  0.1
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.274

Download Data

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

  Natural Product: NPC277098

Natural Product ID:  NPC277098
Common Name*:   XZOSNHNAQRVGSZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XZOSNHNAQRVGSZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H11N5O2/c1-12-4(3-13)2-10-5(6(12)14)11-7(8)9/h2,13H,3H2,1H3,(H4,8,9,10,11)
SMILES:  Cn1c(c[nH]c(=NC(=N)N)c1=O)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21780519
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000067] Pyrazines

*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
NPO7645 Helicteres isora Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[4031904]
NPO7645 Helicteres isora Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7645 Helicteres isora Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7645 Helicteres isora Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3844 Parmotrema conformatum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2004 Carausius morosus Species Phasmatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9299.1 Hordeum vulgare subsp. spontaneum Subspecies Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9083 Xanthium chasei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1464 Salix cheilophila Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6869 Ophioderma longicauda Species Ophiodermatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2604 Myrsine pellucida Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25851 Neonauclea schlechteri Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7645 Helicteres isora Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO572 Stizolobium hassjoo n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO135 Zephyranthes rosea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5583 Poria pearsonii Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8464 Ocotea variabilis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6306 Benthosema fibulata Species Myctophidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7200 Spongia gossypina Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9340 Lindackeria dentata Species Achariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1283 Orbignya phalerata 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 NPC277098 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 NPC277098 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