Natural Product: NPC79900

Natural Product IDNPC79900
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
QNXZSNCVVMAUPA-OZYOAYBNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL510739
PubChem CID 9988975
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

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey QNXZSNCVVMAUPA-OZYOAYBNSA-N
Standard InCHI InChI=1S/C56H90O29/c1-19-7-10-56(75-17-19)20(2)31-45(85-56)37(67)32-22-6-5-21-11-26(24(61)12-55(21,4)23(22)8-9-54(31,32)3)76-50-42(72)39(69)44(30(16-60)80-50)81-53-48(47(36(66)29(15-59)79-53)83-49-40(70)33(63)25(62)18-74-49)84-52-43(73)46(35(65)28(14-58)78-52)82-51-41(71)38(68)34(64)27(13-57)77-51/h5,19-20,22-53,57-73H,6-18H2,1-4H3/t19-,20+,22-,23+,24-,25-,26-,27-,28-,29-,30-,31+,32-,33+,34-,35-,36-,37+,38+,39-,40-,41-,42-,43-,44+,45-,46+,47+,48-,49+,50-,51+,52+,53+,54-,55+,56-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H]([C@H]([C@H]4[C@@H]5CC=C6C[C@H]([C@@H](C[C@]6(C)[C@H]5CC[C@]34C)O)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[11170659]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[12502329]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27323 Cestrum nocturnum Species Solanaceae 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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC79900 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8596 High Similarity NPC210569
0.7982 Intermediate Similarity NPC31896
0.7917 Intermediate Similarity NPC263359
0.7623 Intermediate Similarity NPC244431
0.7603 Intermediate Similarity NPC32707
0.7143 Intermediate Similarity NPC256983
0.7131 Intermediate Similarity NPC248202
0.713 Intermediate Similarity NPC308459
0.7025 Intermediate Similarity NPC167183
0.6911 Remote Similarity NPC190939
0.6905 Remote Similarity NPC208832
0.6797 Remote Similarity NPC305771
0.6797 Remote Similarity NPC94072
0.6797 Remote Similarity NPC169816
0.6585 Remote Similarity NPC132080
0.6562 Remote Similarity NPC15918
0.6364 Remote Similarity NPC115165
0.6341 Remote Similarity NPC232037
0.6341 Remote Similarity NPC197003
0.626 Remote Similarity NPC473518
0.624 Remote Similarity NPC476112
0.624 Remote Similarity NPC307534
0.619 Remote Similarity NPC477811
0.6107 Remote Similarity NPC220836
0.6047 Remote Similarity NPC470866
0.6016 Remote Similarity NPC97700
0.6016 Remote Similarity NPC184617
0.6016 Remote Similarity NPC30856
0.6 Remote Similarity NPC13193
0.5984 Remote Similarity NPC470862
0.5954 Remote Similarity NPC480556
0.5878 Remote Similarity NPC94086
0.5878 Remote Similarity NPC473817
0.5827 Remote Similarity NPC232611
0.5827 Remote Similarity NPC330026
0.5789 Remote Similarity NPC473505
0.5738 Remote Similarity NPC473601
0.5726 Remote Similarity NPC300557
0.5659 Remote Similarity NPC470864
0.5625 Remote Similarity NPC475625
0.5615 Remote Similarity NPC83137
0.5573 Remote Similarity NPC233433
0.5573 Remote Similarity NPC480553
0.5565 Remote Similarity NPC602423
0.5564 Remote Similarity NPC470867
0.5556 Remote Similarity NPC477807
0.5532 Remote Similarity NPC481190
0.5528 Remote Similarity NPC475351
0.552 Remote Similarity NPC477809
0.5515 Remote Similarity NPC477808
0.5504 Remote Similarity NPC116756
0.542 Remote Similarity NPC480554
0.5385 Remote Similarity NPC32361
0.5385 Remote Similarity NPC309278
0.5338 Remote Similarity NPC84111
0.5338 Remote Similarity NPC287483
0.5338 Remote Similarity NPC470865
0.5323 Remote Similarity NPC14704
0.5267 Remote Similarity NPC475333
0.5267 Remote Similarity NPC470861
0.5267 Remote Similarity NPC224098
0.5267 Remote Similarity NPC208383
0.5194 Remote Similarity NPC151134
0.5188 Remote Similarity NPC92710
0.5168 Remote Similarity NPC481189
0.5161 Remote Similarity NPC470432
0.5161 Remote Similarity NPC230507
0.5133 Remote Similarity NPC329727
0.5116 Remote Similarity NPC6806
0.5115 Remote Similarity NPC51520
0.5115 Remote Similarity NPC303069
0.5115 Remote Similarity NPC475319
0.5101 Remote Similarity NPC329820
0.5075 Remote Similarity NPC218571
0.5075 Remote Similarity NPC487615
0.5036 Remote Similarity NPC232054

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC79900 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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