Natural Product: NPC479073

Natural Product IDNPC479073
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GJIDPIIOUZERFG-ONEWMBNISA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 636981
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000348] Peptides
            • [CHEMONTID:0004831] Oligopeptides

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 GJIDPIIOUZERFG-ONEWMBNISA-N
Standard InCHI InChI=1S/C55H73N9O9S2/c1-33(2)28-42-49(66)58-41(24-27-75(6)73)55(72)64-25-15-22-46(64)53(70)62-44(30-36-18-11-8-12-19-36)51(68)60-43(29-35-16-9-7-10-17-35)50(67)61-45(31-37-32-56-39-21-14-13-20-38(37)39)52(69)63-47(34(3)4)54(71)57-40(23-26-74-5)48(65)59-42/h7-14,16-21,32-34,40-47,56H,15,22-31H2,1-6H3,(H,57,71)(H,58,66)(H,59,65)(H,60,68)(H,61,67)(H,62,70)(H,63,69)/t40-,41-,42-,43-,44-,45-,46-,47-,75?/m0/s1
SMILES CC(C)C[C@H]1C(=N[C@@H](CCS(=O)C)C(=O)N2CCC[C@H]2C(=N[C@@H](Cc2ccccc2)C(=N[C@@H](Cc2ccccc2)C(=N[C@@H](Cc2c[nH]c3ccccc23)C(=N[C@@H](C(C)C)C(=N[C@@H](CCSC)C(=N1)O)O)O)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
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[24417583]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. n.a. PMID[26923696]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25114 Linum usitatissimum Species Linaceae 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
NPT21723 Cell line Bone marrow cell n.a. IC50 = 470.0 nM PMID[26923696]

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 NPC479073 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
0.9375 High Similarity NPC479066
0.9271 High Similarity NPC479076
0.9255 High Similarity NPC479075
0.883 High Similarity NPC31385
0.87 High Similarity NPC75726
0.8673 High Similarity NPC479065
0.8265 Intermediate Similarity NPC110602
0.8081 Intermediate Similarity NPC479071
0.6381 Remote Similarity NPC293917
0.6333 Remote Similarity NPC325976
0.6333 Remote Similarity NPC326363
0.6321 Remote Similarity NPC107077
0.6306 Remote Similarity NPC162860
0.6147 Remote Similarity NPC223791
0.6078 Remote Similarity NPC479074
0.604 Remote Similarity NPC487314
0.5982 Remote Similarity NPC54420
0.5887 Remote Similarity NPC489555
0.5849 Remote Similarity NPC479069
0.5701 Remote Similarity NPC213629
0.5701 Remote Similarity NPC489625
0.566 Remote Similarity NPC300315
0.5635 Remote Similarity NPC479574
0.5603 Remote Similarity NPC155143
0.5556 Remote Similarity NPC482001
0.5534 Remote Similarity NPC479072
0.552 Remote Similarity NPC483985
0.5468 Remote Similarity NPC75634
0.5446 Remote Similarity NPC483341
0.5435 Remote Similarity NPC49954
0.5342 Remote Similarity NPC153400
0.5323 Remote Similarity NPC100321
0.5286 Remote Similarity NPC485785
0.5278 Remote Similarity NPC479070
0.5273 Remote Similarity NPC487596
0.5258 Remote Similarity NPC17059
0.5143 Remote Similarity NPC314603
0.5109 Remote Similarity NPC63751

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC479073 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
0.6381 Remote Similarity NPD7621 Clinical (unspecified phase)
0.619 Remote Similarity NPD8110 Clinical (unspecified phase)
0.5887 Remote Similarity NPD8493 Clinical (unspecified phase)
0.5603 Remote Similarity NPD8405 Pre-clinical

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