Structure

Physi-Chem Properties

Molecular Weight:  131.07
Volume:  123.038
LogP:  -2.888
LogD:  -1.585
LogS:  -1.026
# Rotatable Bonds:  3
TPSA:  90.41
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.327
Synthetic Accessibility Score:  2.594
Fsp3:  0.5
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:  -6.489
MDCK Permeability:  0.005663627292960882
Pgp-inhibitor:  0.0
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.042
20% Bioavailability (F20%):  0.078
30% Bioavailability (F30%):  0.043

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.363
Plasma Protein Binding (PPB):  7.684246063232422%
Volume Distribution (VD):  0.718
Pgp-substrate:  87.24092864990234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.062
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.051
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.257
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.014

ADMET: Excretion

Clearance (CL):  3.214
Half-life (T1/2):  0.615

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.049
Drug-inuced Liver Injury (DILI):  0.332
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.189
Carcinogencity:  0.096
Eye Corrosion:  0.004
Eye Irritation:  0.082
Respiratory Toxicity:  0.181

Download Data

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

  Natural Product: NPC178259

Natural Product ID:  NPC178259
Common Name*:   WXOFJMWQRNARBH-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WXOFJMWQRNARBH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H4,5,6,8,9)
SMILES:  CN(CC(=O)O)C(=[NH2+])[NH-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   7058172
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives

*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
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. fruit n.a. PMID[15739361]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. seed n.a. PMID[23845552]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota seeds n.a. n.a. PMID[23999046]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24211545]
NPO12323 Bos taurus Species Bovidae Eukaryota Urine n.a. n.a. PMID[6330305]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[932730]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO31339 Rana nigromaculata, Species Ranidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31367 Canis familiaris Species Canidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3392 Agastache rugosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5114 Canis lupus familiaris Species Canidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO913 Pelophylax plancyi Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5178 Pelophylax nigromaculatus Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3392 Agastache rugosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5178 Pelophylax nigromaculatus Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5114 Canis lupus familiaris Species Canidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO913 Pelophylax plancyi Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12011 Crataegus pinnatifida Species Rosaceae 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 NPC178259 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 NPC178259 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