Structure

Physi-Chem Properties

Molecular Weight:  148.07
Volume:  138.937
LogP:  -1.117
LogD:  -0.744
LogS:  0.453
# Rotatable Bonds:  0
TPSA:  69.92
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.405
Synthetic Accessibility Score:  4.052
Fsp3:  1.0
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:  -5.121
MDCK Permeability:  0.00013522894005291164
Pgp-inhibitor:  0.001
Pgp-substrate:  0.901
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.453

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.275
Plasma Protein Binding (PPB):  9.014602661132812%
Volume Distribution (VD):  1.11
Pgp-substrate:  82.2119140625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.171
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.771
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.129
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.135
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.095

ADMET: Excretion

Clearance (CL):  3.394
Half-life (T1/2):  0.755

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.102
Drug-inuced Liver Injury (DILI):  0.038
AMES Toxicity:  0.327
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.333
Carcinogencity:  0.134
Eye Corrosion:  0.025
Eye Irritation:  0.913
Respiratory Toxicity:  0.446

Download Data

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

  Natural Product: NPC126614

Natural Product ID:  NPC126614
Common Name*:   KYPWIZMAJMNPMJ-VANKVMQKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KYPWIZMAJMNPMJ-VANKVMQKSA-N
Standard InCHI:  InChI=1S/C6H12O4/c1-3-4(7)2-5(8)6(9)10-3/h3-9H,2H2,1H3/t3-,4+,5+,6+/m1/s1
SMILES:  C[C@@H]1[C@H](C[C@@H]([C@@H](O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   448819
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

*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
NPO2415 Clathria lissosclera Species n.a. n.a. n.a. n.a. n.a. PMID[11975512]
NPO4280 Inula hupehensis Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[21894898]
NPO4280 Inula hupehensis Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[21894898]
NPO7459 Berberis actinacantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7459 Berberis actinacantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4280 Inula hupehensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7459 Berberis actinacantha Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2415 Clathria lissosclera Species n.a. n.a. 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 NPC126614 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 NPC126614 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