Natural Product: NPC71782

Natural Product IDNPC71782
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YKXRYBDEVKVZKS-DNDSGMOKSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

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 YKXRYBDEVKVZKS-DNDSGMOKSA-N
Standard InCHI InChI=1S/C45H89NO10/c1-3-5-7-9-11-13-15-16-17-18-19-20-21-23-25-27-29-31-33-38(49)44(54)46-36(35-55-45-43(53)42(52)41(51)39(34-47)56-45)40(50)37(48)32-30-28-26-24-22-14-12-10-8-6-4-2/h36-43,45,47-53H,3-35H2,1-2H3,(H,46,54)/t36-,37+,38+,39+,40-,41-,42-,43-,45+/m0/s1
SMILES CCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@@H](CO[C@H]1[C@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)[C@@H]([C@@H](CCCCCCCCCCCCC)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
NPO10828 Adina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[15043423]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[29182349]
NPO10828 Adina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4490 Cephalotaxus sinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10409 Methanothermobacter thermautotrophicus Species Methanobacteriaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO10828 Adina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21552 Oreaster nodosus Species Oreasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7956 Discaria chacaye Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5447 Digitalis canariensis Species Plantaginaceae 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 NPC71782 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
0.9091 High Similarity NPC61894
0.9091 High Similarity NPC297079
0.7258 Intermediate Similarity NPC263545
0.7258 Intermediate Similarity NPC473950
0.7258 Intermediate Similarity NPC111567
0.7258 Intermediate Similarity NPC186840
0.7258 Intermediate Similarity NPC144916
0.7258 Intermediate Similarity NPC486421
0.7258 Intermediate Similarity NPC309898
0.7258 Intermediate Similarity NPC273493
0.7258 Intermediate Similarity NPC475125
0.7258 Intermediate Similarity NPC486419
0.7258 Intermediate Similarity NPC15851
0.7258 Intermediate Similarity NPC115448
0.7258 Intermediate Similarity NPC20819
0.7258 Intermediate Similarity NPC486418
0.7258 Intermediate Similarity NPC473604
0.7258 Intermediate Similarity NPC486420
0.7258 Intermediate Similarity NPC479188
0.7258 Intermediate Similarity NPC81468
0.7031 Intermediate Similarity NPC156782
0.7031 Intermediate Similarity NPC54961
0.6923 Remote Similarity NPC158445
0.6923 Remote Similarity NPC157353
0.6923 Remote Similarity NPC282088
0.6716 Remote Similarity NPC3568
0.6716 Remote Similarity NPC17290
0.6716 Remote Similarity NPC192066
0.6716 Remote Similarity NPC256570
0.6338 Remote Similarity NPC8098
0.6338 Remote Similarity NPC183449
0.6338 Remote Similarity NPC197294
0.6212 Remote Similarity NPC282705
0.6212 Remote Similarity NPC182632
0.6154 Remote Similarity NPC43074
0.6154 Remote Similarity NPC139782
0.6154 Remote Similarity NPC74672
0.6154 Remote Similarity NPC209047
0.597 Remote Similarity NPC242503
0.5616 Remote Similarity NPC23454
0.5616 Remote Similarity NPC70323
0.5616 Remote Similarity NPC262312
0.5616 Remote Similarity NPC35269
0.5556 Remote Similarity NPC145627
0.5541 Remote Similarity NPC45313
0.5325 Remote Similarity NPC201128
0.5211 Remote Similarity NPC475603
0.5211 Remote Similarity NPC600808
0.5179 Remote Similarity NPC606861
0.5179 Remote Similarity NPC607126
0.5085 Remote Similarity NPC217095
0.5085 Remote Similarity NPC264417
0.5085 Remote Similarity NPC195165
0.507 Remote Similarity NPC476523

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC71782 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
0.6154 Remote Similarity NPD8522 Clinical (unspecified phase)

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