Structure

Physi-Chem Properties

Molecular Weight:  902.49
Volume:  874.012
LogP:  1.853
LogD:  2.134
LogS:  -3.162
# Rotatable Bonds:  12
TPSA:  287.14
# H-Bond Aceptor:  18
# H-Bond Donor:  11
# Rings:  8
# Heavy Atoms:  18

MedChem Properties

QED Drug-Likeness Score:  0.107
Synthetic Accessibility Score:  6.319
Fsp3:  0.956
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.366
MDCK Permeability:  0.00015790849283803254
Pgp-inhibitor:  0.266
Pgp-substrate:  0.824
Human Intestinal Absorption (HIA):  0.998
20% Bioavailability (F20%):  0.822
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.053
Plasma Protein Binding (PPB):  62.323158264160156%
Volume Distribution (VD):  0.045
Pgp-substrate:  13.430912971496582%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.331
CYP2C19-inhibitor:  0.003
CYP2C19-substrate:  0.115
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.005
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.059
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.011

ADMET: Excretion

Clearance (CL):  0.518
Half-life (T1/2):  0.765

ADMET: Toxicity

hERG Blockers:  0.584
Human Hepatotoxicity (H-HT):  0.178
Drug-inuced Liver Injury (DILI):  0.023
AMES Toxicity:  0.112
Rat Oral Acute Toxicity:  0.099
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.928
Carcinogencity:  0.25
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC116280

Natural Product ID:  NPC116280
Common Name*:   KNZSXKKCTOYLSV-JPHOUZCVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KNZSXKKCTOYLSV-JPHOUZCVSA-N
Standard InCHI:  InChI=1S/C45H74O18/c1-19(18-57-40-37(54)35(52)32(49)28(16-46)60-40)8-13-45(56)20(2)30-27(63-45)15-26-24-7-6-22-14-23(9-11-43(22,4)25(24)10-12-44(26,30)5)59-42-39(36(53)33(50)29(17-47)61-42)62-41-38(55)34(51)31(48)21(3)58-41/h6,19-21,23-42,46-56H,7-18H2,1-5H3/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29-,30+,31+,32-,33-,34-,35+,36+,37-,38-,39-,40-,41+,42-,43+,44+,45-/m1/s1
SMILES:  C[C@H](CC[C@@]1([C@@H](C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101400564
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal saponins

*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
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11599360]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. seed n.a. PMID[21381697]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7639 Senecio isatideus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2263 Croton megistocarpus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14100 Persea kusanoi Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8075 Cacospongia scalaris Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1158 Isochrysis galbana Species Isochrysidaceae 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 NPC116280 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 NPC116280 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