Structure

Physi-Chem Properties

Molecular Weight:  492.18
Volume:  446.546
LogP:  -1.364
LogD:  -0.588
LogS:  -1.332
# Rotatable Bonds:  6
TPSA:  207.99
# H-Bond Aceptor:  13
# H-Bond Donor:  8
# Rings:  4
# Heavy Atoms:  13

MedChem Properties

QED Drug-Likeness Score:  0.167
Synthetic Accessibility Score:  5.281
Fsp3:  0.81
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.324
MDCK Permeability:  0.00022991989681031555
Pgp-inhibitor:  0.002
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.976
20% Bioavailability (F20%):  0.083
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.205
Plasma Protein Binding (PPB):  23.42992401123047%
Volume Distribution (VD):  0.381
Pgp-substrate:  48.00810241699219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.018
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.129
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.021
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.074
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.014

ADMET: Excretion

Clearance (CL):  1.111
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.157
Drug-inuced Liver Injury (DILI):  0.959
AMES Toxicity:  0.111
Rat Oral Acute Toxicity:  0.339
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.11
Carcinogencity:  0.686
Eye Corrosion:  0.003
Eye Irritation:  0.053
Respiratory Toxicity:  0.942

Download Data

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

  Natural Product: NPC123685

Natural Product ID:  NPC123685
Common Name*:   GKYZLSXVWCJFOK-INEXIVGBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GKYZLSXVWCJFOK-INEXIVGBSA-N
Standard InCHI:  InChI=1S/C21H32O13/c1-7-13(24)15(26)17(28)20(31-7)32-10-4-8(5-22)12-9(10)2-3-30-19(12)34-21-18(29)16(27)14(25)11(6-23)33-21/h2-4,7,9-29H,5-6H2,1H3/t7-,9-,10+,11+,12+,13-,14+,15+,16-,17+,18+,19-,20-,21-/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1C=C(CO)[C@@H]2[C@H]1C=CO[C@H]2O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21591416
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0004081] Iridoid O-glycosides

*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
NPO12492 Dictyophora indusiata Species Phallaceae Eukaryota n.a. n.a. n.a. PMID[12502311]
NPO18375 Bauhinia tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19124 Guevaria sodiroi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13581 Daphnandra repandula Species Atherospermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3211 Liatris microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18057 Chlorobium phaeobacteroides Species Chlorobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16962 Dipsacus laciniatus Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24096 Furcraea macrophylla Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17497 Bohadschia koellikeri Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13955 Lippia javanica Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25931 Psammogeton canescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3040 Acanthella carteri Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19265 Metarhizium viride Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22168 Scutellaria rivularis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12492 Dictyophora indusiata Species Phallaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1350 Danaus plexippus Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10035 Ficus pantoniana Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18170 Aconitum miyabei Species Ranunculaceae 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 NPC123685 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 NPC123685 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