Structure

Physi-Chem Properties

Molecular Weight:  184.04
Volume:  171.773
LogP:  0.164
LogD:  -0.235
LogS:  0.195
# Rotatable Bonds:  2
TPSA:  97.99
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.394
Synthetic Accessibility Score:  2.304
Fsp3:  0.125
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.635
MDCK Permeability:  8.305939445563126e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.039
20% Bioavailability (F20%):  0.944
30% Bioavailability (F30%):  0.495

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.038
Plasma Protein Binding (PPB):  59.98231506347656%
Volume Distribution (VD):  0.447
Pgp-substrate:  28.004751205444336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.066
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.049
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.68
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.18
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.032

ADMET: Excretion

Clearance (CL):  15.087
Half-life (T1/2):  0.965

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.353
Drug-inuced Liver Injury (DILI):  0.668
AMES Toxicity:  0.458
Rat Oral Acute Toxicity:  0.031
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.932
Carcinogencity:  0.055
Eye Corrosion:  0.964
Eye Irritation:  0.916
Respiratory Toxicity:  0.123

Download Data

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

  Natural Product: NPC169827

Natural Product ID:  NPC169827
Common Name*:   NDZZRGXLHGDGPN-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NDZZRGXLHGDGPN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H8O5/c9-5-1-4(2-7(11)12)8(13)6(10)3-5/h1,3,9-10,13H,2H2,(H,11,12)
SMILES:  c1c(CC(=O)O)c(c(cc1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   54106329
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000418] Phenylacetic acids
          • [CHEMONTID:0004644] 2(hydroxyphenyl)acetic acids

*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
NPO28075 Crataegus sanguinea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20735 Aconitum balfourii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28075 Crataegus sanguinea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20735 Aconitum balfourii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23154 Paysonia grandiflora Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27920 Piper kwashoense Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20735 Aconitum balfourii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28355 Pseudocyphellaria crocata Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28075 Crataegus sanguinea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28249 Macaranga pleiostemon Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27977 Crotalaria verrucosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28692 Pteris undulata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28673 Cucumaria echinata Species Cucumariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28547 Arthrocnemum glaucum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28285 Taxus harringtonia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28657 Incarvillea mairei Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29355 Asaemia axillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24825 Colchicum bulbocodium Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28237 Miconia langsdorffii Species Melastomataceae 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 NPC169827 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 NPC169827 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