Structure

Physi-Chem Properties

Molecular Weight:  196.06
Volume:  171.228
LogP:  -2.669
LogD:  -2.58
LogS:  0.101
# Rotatable Bonds:  5
TPSA:  138.45
# H-Bond Aceptor:  7
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.246
Synthetic Accessibility Score:  4.06
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.378
MDCK Permeability:  0.00384759483858943
Pgp-inhibitor:  0.004
Pgp-substrate:  0.49
Human Intestinal Absorption (HIA):  0.39
20% Bioavailability (F20%):  0.583
30% Bioavailability (F30%):  0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.607
Plasma Protein Binding (PPB):  11.653548240661621%
Volume Distribution (VD):  0.681
Pgp-substrate:  77.7231216430664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.023
CYP2C19-inhibitor:  0.009
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.081
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.087
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  1.225
Half-life (T1/2):  0.914

ADMET: Toxicity

hERG Blockers:  0.197
Human Hepatotoxicity (H-HT):  0.118
Drug-inuced Liver Injury (DILI):  0.711
AMES Toxicity:  0.053
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.04
Carcinogencity:  0.003
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.026

Download Data

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

  Natural Product: NPC165798

Natural Product ID:  NPC165798
Common Name*:   RGHNJXZEOKUKBD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RGHNJXZEOKUKBD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)
SMILES:  C(C(C(C(C(C(=O)O)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   604
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000299] Medium-chain hydroxy 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
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26081757]
NPO17612 Xanthium sibiricum Species Asteraceae Eukaryota Fruits n.a. n.a. PMID[26110443]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[27169184]
NPO17612 Xanthium sibiricum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17612 Xanthium sibiricum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17612 Xanthium sibiricum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17612 Xanthium sibiricum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17612 Xanthium sibiricum Species Asteraceae 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
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 37.6 % PMID[496638]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 11.54 % PMID[496639]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.4 % PMID[496640]

☑ 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 NPC165798 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 NPC165798 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