Natural Product: NPC488513

Natural Product IDNPC488513
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
LAKXMIQNJSJBRG-PBSDVJIDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44584164
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene 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 LAKXMIQNJSJBRG-PBSDVJIDSA-N
Standard InCHI InChI=1S/C100H160O53/c1-14-95(9,153-87-75(129)78(50(34-137-87)141-55(109)22-36(2)3)148-89-71(125)64(118)60(114)47(27-101)142-89)20-15-16-37(4)82(130)145-54-26-100(93(131)152-92-80(66(120)62(116)49(144-92)32-136-83-70(124)63(117)56(110)38(5)139-83)150-88-73(127)67(121)76(39(6)140-88)146-86-74(128)77(46(107)31-134-86)147-84-68(122)57(111)43(104)28-132-84)41(23-94(54,7)8)40-17-18-52-96(10)24-42(103)81(97(11,35-102)51(96)19-21-98(52,12)99(40,13)25-53(100)108)151-90-72(126)65(119)61(115)48(143-90)33-138-91-79(59(113)45(106)30-135-91)149-85-69(123)58(112)44(105)29-133-85/h14,16-17,36,38-39,41-54,56-81,83-92,101-108,110-129H,1,15,18-35H2,2-13H3/b37-16+/t38-,39-,41+,42-,43+,44+,45-,46+,47+,48+,49+,50-,51+,52+,53-,54-,56-,57-,58-,59-,60+,61+,62+,63+,64-,65-,66-,67-,68+,69+,70+,71+,72+,73+,74+,75+,76-,77-,78-,79+,80+,81-,83+,84-,85-,86-,87-,88-,89-,90-,91-,92-,95+,96-,97-,98+,99+,100+/m0/s1
SMILES C=C[C@](C)(CC/C=C(C)/C(=O)O[C@H]1C[C@]2([C@H](CC1(C)C)C1=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H]([C@@](C)(CO)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@@H]2O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO2)O)O)O[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O1)O)O)O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO1)OC(=O)CC(C)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)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
NPO27443 Gymnocladus chinensis Species Fabaceae Eukaryota Fruits n.a. n.a. PMID[7494144]
NPO7631 Gleditsia japonica Species Fabaceae Eukaryota Fruits n.a. n.a. PMID[7494144]
NPO7631 Gleditsia japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7631 Gleditsia japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27443 Gymnocladus chinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7631 Gleditsia japonica Species Fabaceae 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
NPT759 Cell line H9 Homo sapiens IC50 = 14000.0 nM PMID[7494144]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 2700.0 nM PMID[7494144]

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 NPC488513 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
0.7107 Intermediate Similarity NPC329893
0.7024 Intermediate Similarity NPC322904
0.6909 Remote Similarity NPC311178
0.6909 Remote Similarity NPC478559
0.6909 Remote Similarity NPC478560
0.6867 Remote Similarity NPC222951
0.6768 Remote Similarity NPC43589
0.6727 Remote Similarity NPC300655
0.6707 Remote Similarity NPC329878
0.659 Remote Similarity NPC324933
0.6552 Remote Similarity NPC319719
0.6514 Remote Similarity NPC265699
0.6369 Remote Similarity NPC233223
0.6369 Remote Similarity NPC183816
0.6331 Remote Similarity NPC196874
0.6312 Remote Similarity NPC102505
0.6312 Remote Similarity NPC488514
0.631 Remote Similarity NPC484829
0.6201 Remote Similarity NPC488204
0.6167 Remote Similarity NPC488201
0.6023 Remote Similarity NPC45606
0.6022 Remote Similarity NPC187497
0.6011 Remote Similarity NPC100612
0.5988 Remote Similarity NPC220838
0.5966 Remote Similarity NPC475444
0.5966 Remote Similarity NPC473679
0.5963 Remote Similarity NPC309223
0.5963 Remote Similarity NPC144644
0.5963 Remote Similarity NPC170407
0.5906 Remote Similarity NPC488517
0.5899 Remote Similarity NPC113620
0.5866 Remote Similarity NPC472270
0.5866 Remote Similarity NPC112492
0.5849 Remote Similarity NPC237191
0.5818 Remote Similarity NPC68767
0.5806 Remote Similarity NPC174336
0.5697 Remote Similarity NPC224381
0.568 Remote Similarity NPC480421
0.5665 Remote Similarity NPC484831
0.5621 Remote Similarity NPC33012
0.5617 Remote Similarity NPC473452
0.5617 Remote Similarity NPC13998
0.559 Remote Similarity NPC85154
0.5576 Remote Similarity NPC37860
0.5575 Remote Similarity NPC484830
0.5562 Remote Similarity NPC8524
0.5525 Remote Similarity NPC23020
0.5509 Remote Similarity NPC142151
0.5508 Remote Similarity NPC488200
0.5486 Remote Similarity NPC297950
0.5449 Remote Similarity NPC70809
0.5444 Remote Similarity NPC293031
0.5412 Remote Similarity NPC153673
0.5412 Remote Similarity NPC51099
0.5402 Remote Similarity NPC475177
0.538 Remote Similarity NPC815
0.5372 Remote Similarity NPC488203
0.5366 Remote Similarity NPC473386
0.5344 Remote Similarity NPC488202
0.5337 Remote Similarity NPC471577
0.533 Remote Similarity NPC485563
0.5318 Remote Similarity NPC275225
0.5301 Remote Similarity NPC471580
0.5281 Remote Similarity NPC472268
0.5249 Remote Similarity NPC13989
0.5241 Remote Similarity NPC286457
0.522 Remote Similarity NPC207738
0.5189 Remote Similarity NPC488619
0.5146 Remote Similarity NPC220160
0.5146 Remote Similarity NPC267694
0.5091 Remote Similarity NPC480423
0.508 Remote Similarity NPC472269
0.5064 Remote Similarity NPC232237
0.5057 Remote Similarity NPC110385
0.5031 Remote Similarity NPC104137
0.5031 Remote Similarity NPC26626

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488513 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