Natural Product: NPC473679

Natural Product IDNPC473679
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Kinmoonoside B
IUPAC Name [(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5S,6S)-5-[(2R,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-6-methyl-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl] (3S,4aR,5R,6aR,6aS,6bR,8aR,10S,12aR,14bS)-3-[(2E,6S)-6-[(2S,3R,4R,5S,6R)-3,4-dihydroxy-5-[(2E)-6-hydroxy-2-(hydroxymethyl)-6-methylocta-2,7-dienoyl]oxy-6-methyloxan-2-yl]oxy-2-(hydroxymethyl)-6-methylocta-2,7-dienoyl]oxy-10-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-[[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxymethyl]oxan-2-yl]oxy-5-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms kinmoonoside B
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL449004
PubChem CID 44566291
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 ZWQIYSCVPSEGHA-SNMLLMHDSA-N
Standard InCHI InChI=1S/C96H152O47/c1-14-91(9,125)24-16-18-42(32-98)79(123)137-73-39(3)129-85(71(120)66(73)115)143-92(10,15-2)25-17-19-41(31-97)78(122)135-55-30-96(88(124)142-87-77(64(113)59(108)48(35-101)133-87)141-84-72(121)75(139-82-69(118)62(111)57(106)46(33-99)130-82)74(40(4)128-84)138-81-68(117)60(109)49(36-102)132-81)44(28-89(55,5)6)43-20-21-52-93(11)26-23-54(90(7,8)51(93)22-27-94(52,12)95(43,13)29-53(96)104)136-86-76(140-83-70(119)63(112)58(107)47(34-100)131-83)65(114)61(110)50(134-86)38-127-80-67(116)56(105)45(103)37-126-80/h14-15,18-20,39-40,44-77,80-87,97-121,125H,1-2,16-17,21-38H2,3-13H3/b41-19+,42-18+/t39-,40+,44+,45+,46-,47-,48-,49+,50-,51+,52-,53-,54+,55+,56+,57-,58-,59-,60+,61-,62+,63+,64+,65+,66-,67-,68-,69-,70-,71-,72-,73-,74+,75+,76-,77-,80+,81-,82+,83+,84+,85+,86+,87+,91?,92-,93+,94-,95-,96-/m1/s1
SMILES OC[C@H]1O[C@@H](OC(=O)[C@@]23C[C@H](OC(=O)/C(=C/CC[C@](O[C@@H]4O[C@H](C)[C@H]([C@@H]([C@H]4O)O)OC(=O)/C(=C/CCC(C=C)(O)C)/CO)(C=C)C)/CO)C(C[C@H]3C3=CC[C@H]4[C@@]([C@@]3(C[C@H]2O)C)(C)CC[C@@H]2[C@]4(C)CC[C@@H](C2(C)C)O[C@@H]2O[C@H](CO[C@@H]3OC[C@@H]([C@@H]([C@H]3O)O)O)[C@H]([C@@H]([C@H]2O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@H]1O[C@H]([C@@H]([C@H]1O)O)CO

  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
NPO3615 Acacia concinna Species Fabaceae Eukaryota fruits myanmar n.a. PMID[11141109]
NPO3615 Acacia concinna Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3615 Acacia concinna 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
NPT453 Cell line HT-1080 Homo sapiens ED50 = 0.7 uM PMID[20022253]

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 NPC473679 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
1.0 High Similarity NPC475444
0.903 High Similarity NPC475177
0.8733 High Similarity NPC174336
0.8521 High Similarity NPC196874
0.8506 High Similarity NPC187497
0.8446 Intermediate Similarity NPC322904
0.8333 Intermediate Similarity NPC319719
0.8288 Intermediate Similarity NPC222951
0.8252 Intermediate Similarity NPC329878
0.817 Intermediate Similarity NPC488201
0.8069 Intermediate Similarity NPC233223
0.8069 Intermediate Similarity NPC183816
0.8042 Intermediate Similarity NPC484830
0.8014 Intermediate Similarity NPC300655
0.8 Intermediate Similarity NPC484829
0.7986 Intermediate Similarity NPC329893
0.7908 Intermediate Similarity NPC324933
0.7895 Intermediate Similarity NPC100612
0.7881 Intermediate Similarity NPC113620
0.7852 Intermediate Similarity NPC311178
0.7756 Intermediate Similarity NPC488204
0.7692 Intermediate Similarity NPC265699
0.7584 Intermediate Similarity NPC43589
0.75 Intermediate Similarity NPC478559
0.75 Intermediate Similarity NPC478560
0.7312 Intermediate Similarity NPC488202
0.7312 Intermediate Similarity NPC488200
0.72 Intermediate Similarity NPC484831
0.7124 Intermediate Similarity NPC220838
0.6933 Remote Similarity NPC488203
0.6752 Remote Similarity NPC13989
0.6731 Remote Similarity NPC45606
0.625 Remote Similarity NPC488620
0.6242 Remote Similarity NPC23020
0.6127 Remote Similarity NPC207738
0.6036 Remote Similarity NPC472270
0.6036 Remote Similarity NPC112492
0.5966 Remote Similarity NPC488513
0.5858 Remote Similarity NPC488619
0.5855 Remote Similarity NPC470876
0.5799 Remote Similarity NPC488618
0.5793 Remote Similarity NPC472268
0.5743 Remote Similarity NPC123522
0.5686 Remote Similarity NPC286457
0.566 Remote Similarity NPC489209
0.5644 Remote Similarity NPC489208
0.5641 Remote Similarity NPC309223
0.564 Remote Similarity NPC482013
0.5578 Remote Similarity NPC104137
0.5578 Remote Similarity NPC26626
0.5494 Remote Similarity NPC33012
0.5455 Remote Similarity NPC85154
0.5432 Remote Similarity NPC8524
0.5404 Remote Similarity NPC102505
0.5404 Remote Similarity NPC488514
0.5385 Remote Similarity NPC13998
0.5379 Remote Similarity NPC105800
0.5375 Remote Similarity NPC482010
0.5371 Remote Similarity NPC472269
0.5357 Remote Similarity NPC297950
0.531 Remote Similarity NPC232237
0.5287 Remote Similarity NPC473452
0.526 Remote Similarity NPC603137
0.5197 Remote Similarity NPC172365
0.5197 Remote Similarity NPC185466
0.5185 Remote Similarity NPC220160
0.5132 Remote Similarity NPC210729
0.5132 Remote Similarity NPC82931
0.5123 Remote Similarity NPC70809
0.5033 Remote Similarity NPC481079

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473679 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