Natural Product: NPC262796

Natural Product IDNPC262796
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.
Symplocososide L
IUPAC Name (2S,3S,4S,5R,6R)-6-[[(3S,4aR,6aR,6bS,7R,8S,8aR,9R,10R,12aS,14aR,14bR)-10-[(2Z)-3,7-dimethylocta-2,6-dienoyl]oxy-7,8-dihydroxy-8a-(hydroxymethyl)-4,4,6a,6b,11,11,14b-heptamethyl-9-(2-methylpropanoyloxy)-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-4-acetyloxy-3-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
Synonyms symplocososide L
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL498883
PubChem CID 16099389
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 XPBNJNXKQVWGAY-XWVGWLPGSA-N
Standard InCHI InChI=1S/C63H98O24/c1-28(2)15-14-16-30(5)23-39(68)83-51-52(87-54(78)29(3)4)63(27-66)33(24-58(51,7)8)32-17-18-37-60(11)21-20-38(59(9,10)36(60)19-22-61(37,12)62(32,13)49(74)50(63)75)82-57-48(86-56-44(73)42(71)40(69)34(25-64)80-56)46(79-31(6)67)45(47(85-57)53(76)77)84-55-43(72)41(70)35(26-65)81-55/h15,17,23,29,33-38,40-52,55-57,64-66,69-75H,14,16,18-22,24-27H2,1-13H3,(H,76,77)/b30-23-/t33-,34+,35-,36-,37+,38-,40+,41-,42-,43+,44+,45-,46-,47-,48+,49-,50+,51-,52-,55-,56-,57+,60-,61+,62-,63-/m0/s1
SMILES CC(=CCC/C(=CC(=O)O[C@H]1[C@@H]([C@@]2(CO)[C@@H](CC1(C)C)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)[C@H]([C@H]2O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O)OC(=O)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC(=O)C(C)C)/C)C

  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
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota roots n.a. n.a. PMID[15620235]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota roots Nanning City, Guangxi Province, People's Republic of China 1997-Jan PMID[17190442]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8121 Symplocos chinensis Species Symplocaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8121 Symplocos chinensis Species Symplocaceae 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
NPT180 Cell line HCT-8 Homo sapiens IC50 = 1700.0 nM PubChem BioAssay data set
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 2700.0 nM PubChem BioAssay data set
NPT547 Cell line BGC-823 Homo sapiens IC50 > 10000.0 nM PubChem BioAssay data set
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[21868221]
NPT179 Cell line A2780 Homo sapiens IC50 = 2400.0 nM PMID[22440015]

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 NPC262796 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 NPC45346
0.9459 High Similarity NPC475377
0.9459 High Similarity NPC476074
0.8496 Intermediate Similarity NPC264566
0.8361 Intermediate Similarity NPC150893
0.7769 Intermediate Similarity NPC484833
0.7583 Intermediate Similarity NPC329923
0.7583 Intermediate Similarity NPC475281
0.7583 Intermediate Similarity NPC475167
0.752 Intermediate Similarity NPC329960
0.6975 Remote Similarity NPC329976
0.6825 Remote Similarity NPC134914
0.6719 Remote Similarity NPC329993
0.6718 Remote Similarity NPC295408
0.6612 Remote Similarity NPC477078
0.6565 Remote Similarity NPC173435
0.6565 Remote Similarity NPC172374
0.6565 Remote Similarity NPC478064
0.6308 Remote Similarity NPC178264
0.6308 Remote Similarity NPC473755
0.6279 Remote Similarity NPC46823
0.6231 Remote Similarity NPC192765
0.6124 Remote Similarity NPC478150
0.6119 Remote Similarity NPC329657
0.608 Remote Similarity NPC477077
0.6048 Remote Similarity NPC470914
0.5985 Remote Similarity NPC301639
0.5985 Remote Similarity NPC478065
0.5984 Remote Similarity NPC605294
0.5938 Remote Similarity NPC25998
0.5814 Remote Similarity NPC478152
0.5814 Remote Similarity NPC478151
0.5789 Remote Similarity NPC470912
0.5789 Remote Similarity NPC473918
0.5785 Remote Similarity NPC603026
0.576 Remote Similarity NPC470913
0.5752 Remote Similarity NPC473586
0.5748 Remote Similarity NPC477075
0.5672 Remote Similarity NPC277212
0.5672 Remote Similarity NPC30279
0.563 Remote Similarity NPC71391
0.563 Remote Similarity NPC329828
0.562 Remote Similarity NPC475513
0.562 Remote Similarity NPC225791
0.5615 Remote Similarity NPC606553
0.5597 Remote Similarity NPC602995
0.5507 Remote Similarity NPC312650
0.5435 Remote Similarity NPC488308
0.5423 Remote Similarity NPC488309
0.5417 Remote Similarity NPC69425
0.5396 Remote Similarity NPC271610
0.5299 Remote Similarity NPC609119
0.5267 Remote Similarity NPC477076
0.5224 Remote Similarity NPC107536
0.5224 Remote Similarity NPC280029
0.5224 Remote Similarity NPC9470
0.5143 Remote Similarity NPC470518
0.5039 Remote Similarity NPC605226
0.5036 Remote Similarity NPC478600
0.5036 Remote Similarity NPC478599
0.5035 Remote Similarity NPC478598

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC262796 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