Natural Product: NPC254133

Natural Product IDNPC254133
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
QZNIVVAKPLIDJX-IBVWZRLASA-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:0000257] Sphingolipids
        • [CHEMONTID:0003258] Glycosphingolipids

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 QZNIVVAKPLIDJX-IBVWZRLASA-N
Standard InCHI InChI=1S/C48H93NO10/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-41(52)47(57)49-39(38-58-48-46(56)45(55)44(54)42(37-50)59-48)43(53)40(51)35-33-31-29-27-25-16-14-12-10-8-6-4-2/h27,29,39-46,48,50-56H,3-26,28,30-38H2,1-2H3,(H,49,57)/b29-27-/t39-,40-,41-,42-,43+,44-,45+,46-,48-/m1/s1
SMILES CCCCCCCCCCCCCCCCCCCCCC[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](CCC/C=CCCCCCCCCC)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
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. PMID[15387653]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. PMID[22325941]
NPO23779 Premna subscandens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24926 Fomes fomentarius Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24970 Anthurium versicolor Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21600 Aconitum variegatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20584 Cheilanthes fragrans Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21344 Fadogia agrestis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24525 Desmanthodium perfoliatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21534 Ostrya carpinifolia Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25276 Ligusticum scoticum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21600 Aconitum variegatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21600 Aconitum variegatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23779 Premna subscandens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25276 Ligusticum scoticum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21600 Aconitum variegatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23662 Arthraxon hispidus Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25276 Ligusticum scoticum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25139 Cocculus sarmentosus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23523 Triumfetta cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23662 Arthraxon hispidus Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24926 Fomes fomentarius Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24729 Securinega tinctoria Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23323 Dianthus superbus Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25276 Ligusticum scoticum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21534 Ostrya carpinifolia Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24970 Anthurium versicolor Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24685 Ramalina dilacerata Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24525 Desmanthodium perfoliatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23779 Premna subscandens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20584 Cheilanthes fragrans Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21600 Aconitum variegatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22500 Stephania dielsiana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21344 Fadogia agrestis Species Rubiaceae 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 NPC254133 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 NPC61894
1.0 High Similarity NPC297079
0.8065 Intermediate Similarity NPC263545
0.8065 Intermediate Similarity NPC473950
0.8065 Intermediate Similarity NPC111567
0.8065 Intermediate Similarity NPC186840
0.8065 Intermediate Similarity NPC144916
0.8065 Intermediate Similarity NPC486421
0.8065 Intermediate Similarity NPC309898
0.8065 Intermediate Similarity NPC273493
0.8065 Intermediate Similarity NPC475125
0.8065 Intermediate Similarity NPC486419
0.8065 Intermediate Similarity NPC15851
0.8065 Intermediate Similarity NPC115448
0.8065 Intermediate Similarity NPC20819
0.8065 Intermediate Similarity NPC486418
0.8065 Intermediate Similarity NPC473604
0.8065 Intermediate Similarity NPC486420
0.8065 Intermediate Similarity NPC479188
0.8065 Intermediate Similarity NPC81468
0.7692 Intermediate Similarity NPC158445
0.7692 Intermediate Similarity NPC157353
0.7692 Intermediate Similarity NPC282088
0.7538 Intermediate Similarity NPC156782
0.7538 Intermediate Similarity NPC54961
0.7042 Intermediate Similarity NPC8098
0.7042 Intermediate Similarity NPC183449
0.7042 Intermediate Similarity NPC197294
0.697 Remote Similarity NPC282705
0.697 Remote Similarity NPC182632
0.6716 Remote Similarity NPC242503
0.6714 Remote Similarity NPC3568
0.6714 Remote Similarity NPC17290
0.6714 Remote Similarity NPC192066
0.6714 Remote Similarity NPC256570
0.6667 Remote Similarity NPC43074
0.6667 Remote Similarity NPC139782
0.6667 Remote Similarity NPC74672
0.6667 Remote Similarity NPC209047
0.6081 Remote Similarity NPC23454
0.6081 Remote Similarity NPC70323
0.6081 Remote Similarity NPC262312
0.6081 Remote Similarity NPC35269
0.6 Remote Similarity NPC45313
0.5932 Remote Similarity NPC217095
0.5932 Remote Similarity NPC264417
0.5915 Remote Similarity NPC475603
0.5915 Remote Similarity NPC600808
0.5769 Remote Similarity NPC201128
0.5479 Remote Similarity NPC602861
0.5405 Remote Similarity NPC473581
0.5286 Remote Similarity NPC488689
0.5147 Remote Similarity NPC469469
0.5085 Remote Similarity NPC145627
0.5068 Remote Similarity NPC21693

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC254133 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
0.6667 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