Natural Product: NPC473505

Natural Product IDNPC473505
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BTSNKLNQWIMUMJ-BRSIHUFTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL444026
PubChem CID 44558942
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 BTSNKLNQWIMUMJ-BRSIHUFTSA-N
Standard InCHI InChI=1S/C55H86O27/c1-20-7-10-55(73-17-20)21(2)34-29(82-55)12-26-24-6-5-22-11-23(8-9-53(22,3)25(24)13-33(61)54(26,34)4)74-50-42(69)39(66)44(32(16-58)77-50)78-52-47(46(38(65)31(15-57)76-52)80-49-41(68)36(63)28(60)19-72-49)81-51-43(70)45(37(64)30(14-56)75-51)79-48-40(67)35(62)27(59)18-71-48/h13,20-24,26-32,34-52,56-60,62-70H,5-12,14-19H2,1-4H3/t20?,21-,22-,23-,24+,26-,27+,28+,29-,30+,31+,32+,34-,35-,36-,37+,38+,39+,40+,41+,42+,43+,44-,45-,46-,47+,48-,49-,50+,51-,52-,53-,54+,55+/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2)CC[C@@H]2C3=CC(=O)[C@]3([C@H]2C[C@H]2[C@@H]3[C@H](C)[C@]3(O2)CCC(CO3)C)C)C)[C@@H]([C@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O)O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O)O)O)O

  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
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota aerial parts n.a. n.a. PMID[11087596]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota underground parts n.a. n.a. PMID[12398537]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota fresh tubers n.a. n.a. PMID[14738376]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12929 Polianthes tuberosa Species Asparagaceae 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
NPT116 Cell line HL-60 Homo sapiens IC50 = 6.1 ug.mL-1 DrugMatrix in vitro pharmacology data

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 NPC473505 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
0.7607 Intermediate Similarity NPC94086
0.7607 Intermediate Similarity NPC473817
0.7456 Intermediate Similarity NPC232037
0.7417 Intermediate Similarity NPC220836
0.7355 Intermediate Similarity NPC15918
0.7265 Intermediate Similarity NPC132080
0.7177 Intermediate Similarity NPC305771
0.7177 Intermediate Similarity NPC94072
0.7177 Intermediate Similarity NPC169816
0.6891 Remote Similarity NPC476112
0.6891 Remote Similarity NPC307534
0.6833 Remote Similarity NPC233433
0.6667 Remote Similarity NPC97700
0.6667 Remote Similarity NPC184617
0.6667 Remote Similarity NPC470866
0.6667 Remote Similarity NPC30856
0.65 Remote Similarity NPC475625
0.6406 Remote Similarity NPC210569
0.626 Remote Similarity NPC470864
0.6198 Remote Similarity NPC475319
0.6098 Remote Similarity NPC116756
0.6017 Remote Similarity NPC475351
0.5935 Remote Similarity NPC115165
0.5896 Remote Similarity NPC263359
0.5877 Remote Similarity NPC250393
0.5859 Remote Similarity NPC31896
0.5833 Remote Similarity NPC273002
0.5789 Remote Similarity NPC79900
0.5781 Remote Similarity NPC84111
0.5781 Remote Similarity NPC287483
0.5781 Remote Similarity NPC470865
0.5662 Remote Similarity NPC244431
0.5659 Remote Similarity NPC477811
0.5625 Remote Similarity NPC108072
0.5591 Remote Similarity NPC473518
0.5581 Remote Similarity NPC470862
0.5571 Remote Similarity NPC330026
0.5564 Remote Similarity NPC480556
0.5517 Remote Similarity NPC329727
0.5515 Remote Similarity NPC32707
0.5455 Remote Similarity NPC329807
0.5448 Remote Similarity NPC481189
0.5447 Remote Similarity NPC473601
0.544 Remote Similarity NPC51172
0.544 Remote Similarity NPC49032
0.5426 Remote Similarity NPC232611
0.5424 Remote Similarity NPC206003
0.5424 Remote Similarity NPC473610
0.5391 Remote Similarity NPC470863
0.536 Remote Similarity NPC92890
0.5344 Remote Similarity NPC83137
0.5303 Remote Similarity NPC92297
0.5299 Remote Similarity NPC234352
0.5282 Remote Similarity NPC481190
0.5234 Remote Similarity NPC98018
0.5234 Remote Similarity NPC284104
0.5234 Remote Similarity NPC103616
0.5214 Remote Similarity NPC325828
0.52 Remote Similarity NPC202898
0.5185 Remote Similarity NPC470867
0.517 Remote Similarity NPC329820
0.5164 Remote Similarity NPC107962
0.5159 Remote Similarity NPC602423
0.5109 Remote Similarity NPC248202
0.5078 Remote Similarity NPC300557
0.5075 Remote Similarity NPC256983
0.5072 Remote Similarity NPC477807
0.504 Remote Similarity NPC14704
0.5038 Remote Similarity NPC480554
0.5036 Remote Similarity NPC477808

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473505 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
0.5214 Remote Similarity NPD8171 Phase 2
0.5122 Remote Similarity NPD8170 Phase 2

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