Natural Product: NPC611721

Natural Product IDNPC611721
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VQFKFAKEUMHBLV-BYSUZVQFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL384200
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 VQFKFAKEUMHBLV-BYSUZVQFSA-N
Standard InCHI InChI=1S/C50H99NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-45(54)51-42(41-59-50-49(58)48(57)47(56)44(40-52)60-50)46(55)43(53)38-36-34-32-30-28-16-14-12-10-8-6-4-2/h42-44,46-50,52-53,55-58H,3-41H2,1-2H3,(H,51,54)/t42-,43+,44+,46-,47-,48-,49+,50-/m0/s1
SMILES CCCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@H](O)CCCCCCCCCCCCCC

  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
NPO33620 Agelas mauritianus Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[7783149]
NPO33620 Agelas mauritianus Species Agelasidae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT28465 Single protein Antigen-presenting glycoprotein CD1d Homo sapiens Activity n.a. n.a. n.a. PMID[21145749]
NPT28465 Single protein Antigen-presenting glycoprotein CD1d Homo sapiens Activity n.a. n.a. n.a. PMID[20061147]
NPT28465 Single protein Antigen-presenting glycoprotein CD1d Homo sapiens Activity n.a. n.a. n.a. PMID[31185411]
NPT28465 Single protein Antigen-presenting glycoprotein CD1d Homo sapiens Activity n.a. n.a. n.a. PMID[26985293]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[19535248]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[19580320]
NPT891 Cell line iNKT n.a. Activity = 4.1 % PMID[25941558]
NPT891 Cell line iNKT n.a. Activity = 34.0 % PMID[20529677]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[18993065]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[18586489]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[17608465]
NPT2735 Cell line RAW Mus musculus Activity n.a. n.a. n.a. PMID[19502056]
NPT3722 Cell line 4T1 Mus musculus Activity n.a. n.a. n.a. PMID[17566107]
NPT891 Cell line iNKT n.a. Activity = 26.0 % PMID[20462758]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[28626526]
NPT319 Cell line B16 Mus musculus Control = 86.7 % PMID[7783149]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[24900444]
NPT891 Cell line iNKT n.a. EC50 = 2700.0 nM PMID[19580320]
NPT319 Cell line B16 Mus musculus Control = 53.8 % PMID[7783149]
NPT319 Cell line B16 Mus musculus Control = 67.6 % PMID[7783149]
NPT891 Cell line iNKT n.a. Activity n.a. n.a. n.a. PMID[31185411]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[22243602]
NPT28438 Unchecked Unchecked n.a. Activity = 1.9 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 1.8 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[24900836]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[26985293]
NPT28438 Unchecked Unchecked n.a. Activity = 3.5 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 2.9 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 68.0 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[19502056]
NPT30114 Cell line Splenocyte Mus musculus Activity = 0.9 ng/ml PMID[17266209]
NPT28438 Unchecked Unchecked n.a. Activity = 569.0 % PMID[17419054]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[27325450]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[24900347]
NPT28438 Unchecked Unchecked n.a. Activity = 2.3 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 7.3 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 10.8 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 30.0 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 3.4 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 7.7 n.a. PMID[17566107]
NPT30114 Cell line Splenocyte Mus musculus Activity n.a. n.a. n.a. PMID[24900347]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[21439833]
NPT28438 Unchecked Unchecked n.a. Kd = 350.0 nM PMID[17608465]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[31097989]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 6.6 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 32.0 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 1.6 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 0.9 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 128.0 % PMID[17419054]
NPT28438 Unchecked Unchecked n.a. Activity = 2.6 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 3.9 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 1.2 n.a. PMID[17566107]
NPT30114 Cell line Splenocyte Mus musculus Activity = 12.8 ng/ml PMID[17266209]
NPT30114 Cell line Splenocyte Mus musculus Activity = 15.6 ng/ml PMID[17266209]
NPT30114 Cell line Splenocyte Mus musculus Activity = 1.12 ng/ml PMID[17266209]
NPT28438 Unchecked Unchecked n.a. Activity = 1.4 n.a. PMID[17566107]
NPT28438 Unchecked Unchecked n.a. Activity = 1.7 n.a. PMID[17566107]
NPT30114 Cell line Splenocyte Mus musculus Activity = 569.0 % PMID[22480852]
NPT30114 Cell line Splenocyte Mus musculus Activity = 128.0 % PMID[22480852]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity n.a. n.a. n.a. PMID[17566107]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition n.a. n.a. % PMID[20660669]
NPT29415 Protein family Antigen-presenting glycoprotein CD1d Mus musculus Ratio = 0.45 % PMID[31982233]
NPT29415 Protein family Antigen-presenting glycoprotein CD1d Mus musculus Activity n.a. n.a. n.a. PMID[31786009]
NPT29415 Protein family Antigen-presenting glycoprotein CD1d Mus musculus Activity n.a. n.a. n.a. PMID[31097998]
NPT30089 Cell line T-cell n.a. Activity n.a. n.a. n.a. PMID[18790646]
NPT29415 Protein family Antigen-presenting glycoprotein CD1d Mus musculus Ratio < 0.02 % PMID[31982233]
NPT605 Organism Homo sapiens Homo sapiens Control = 389.0 % PMID[7783149]
NPT605 Organism Homo sapiens Homo sapiens Control = 590.0 % PMID[7783149]
NPT605 Organism Homo sapiens Homo sapiens Control = 398.0 % PMID[7783149]
NPT605 Organism Homo sapiens Homo sapiens Control = 663.0 % PMID[7783149]
NPT605 Organism Homo sapiens Homo sapiens Control = 356.0 % PMID[7783149]
NPT605 Organism Homo sapiens Homo sapiens Control = 581.0 % PMID[7783149]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Inhibition n.a. n.a. % PMID[20660669]
NPT29415 Protein family Antigen-presenting glycoprotein CD1d Mus musculus Ratio = 0.66 % PMID[31982233]
NPT29131 Unknown Molecular identity unknown n.a. Activity n.a. n.a. n.a. PMID[19502056]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 58.9 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 3.6 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 13.1 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 5.5 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[17266209]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[19580320]
NPT32 Organism Mus musculus Mus musculus Ratio = 13.2 n.a. PMID[31786009]
NPT32 Organism Mus musculus Mus musculus Ratio = 2.5 n.a. PMID[31786009]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[23602521]
NPT32 Organism Mus musculus Mus musculus Activity = 2.6 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[18993065]
NPT32 Organism Mus musculus Mus musculus Activity = 3.2 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Control = 251.0 % PMID[7783149]
NPT32 Organism Mus musculus Mus musculus Activity = 2.8 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[23919244]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[24900836]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[31786009]
NPT32 Organism Mus musculus Mus musculus Ratio = 2.8 n.a. PMID[30783507]
NPT32 Organism Mus musculus Mus musculus Activity = 1450.0 pg/ml PMID[21392982]
NPT32 Organism Mus musculus Mus musculus TGIR = 50.9 % DOI[10.1016/0960-894X(95)00098-E]
NPT32 Organism Mus musculus Mus musculus Incorporation = 17438.0 c.p.m. PMID[10346936]
NPT32 Organism Mus musculus Mus musculus Activity = 12145.0 pg/ml PMID[21392982]
NPT32 Organism Mus musculus Mus musculus Ratio = 8.35 n.a. PMID[21392982]
NPT32 Organism Mus musculus Mus musculus Incorporation = 17636.0 c.p.m. PMID[10346936]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[30783507]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[26985293]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[25941558]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[28626526]
NPT32 Organism Mus musculus Mus musculus Activity = 7.8 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 18.7 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[21439833]
NPT32 Organism Mus musculus Mus musculus Activity = 240.0 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Control = 200.0 % PMID[7783149]
NPT32 Organism Mus musculus Mus musculus Control = 125.0 % PMID[7783149]
NPT32 Organism Mus musculus Mus musculus Ratio = 0.0043 n.a. DOI[10.1039/C3MD00073G]
NPT32 Organism Mus musculus Mus musculus Control = 283.0 % PMID[7783149]
NPT32 Organism Mus musculus Mus musculus Activity = 300.0 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[22739091]
NPT32 Organism Mus musculus Mus musculus Incorporation = 13499.0 c.p.m. PMID[10346936]
NPT32 Organism Mus musculus Mus musculus TGIR = 40.2 % DOI[10.1016/0960-894X(95)00098-E]
NPT32 Organism Mus musculus Mus musculus Activity = 2925.0 pg/ml PMID[31786009]
NPT32 Organism Mus musculus Mus musculus Activity = 30.5 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 15.1 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 2127.0 pg/ml PMID[25941558]
NPT32 Organism Mus musculus Mus musculus Ratio = 1.0 n.a. PMID[30935793]
NPT32 Organism Mus musculus Mus musculus Activity = 51.0 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 3.0 n.a. PMID[17566107]
NPT32 Organism Mus musculus Mus musculus Activity = 1331.0 pg/ml PMID[30935793]
NPT32 Organism Mus musculus Mus musculus Activity = 666.08 pg/ml/hr PMID[30935793]
NPT32 Organism Mus musculus Mus musculus TGIR = 41.1 % DOI[10.1016/0960-894X(95)00098-E]
NPT32 Organism Mus musculus Mus musculus TGIR = 51.1 % DOI[10.1016/0960-894X(95)00098-E]
NPT32 Organism Mus musculus Mus musculus Activity = 17380.41 pg/ml PMID[30935793]
NPT32 Organism Mus musculus Mus musculus Activity = 280.0 pg/ml/hr PMID[30935793]
NPT32 Organism Mus musculus Mus musculus Ratio = 12.1 n.a. PMID[30783507]
NPT33 Organism Japanese encephalitis virus Japanese encephalitis virus Survival = 57.0 % PMID[20660669]





 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 NPC611721 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
0.7302 Intermediate Similarity NPC476523
0.7188 Intermediate Similarity NPC475603
0.7188 Intermediate Similarity NPC600808
0.5789 Remote Similarity NPC477198
0.5714 Remote Similarity NPC602861
0.5634 Remote Similarity NPC473581
0.5217 Remote Similarity NPC604832
0.5195 Remote Similarity NPC604736
0.5088 Remote Similarity NPC608665

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC611721 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