Natural Product: NPC256213

Natural Product IDNPC256213
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KZQOMXKLASFQRY-JSOSNVBQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 15432817
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related 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 KZQOMXKLASFQRY-JSOSNVBQSA-N
Standard InCHI InChI=1S/C39H45N2O6/c1-40-16-14-27-22-36(44-6)38(45-7)39-37(27)30(40)18-25-10-13-32(42-4)34(20-25)46-28-11-8-24(9-12-28)19-31-29-23-35(47-39)33(43-5)21-26(29)15-17-41(31,2)3/h8-13,20-23,30-31H,14-19H2,1-7H3/q+1/t30-,31+/m1/s1
SMILES CN1CCc2cc(c(c3c2[C@H]1Cc1ccc(c(c1)Oc1ccc(cc1)C[C@H]1c2cc(c(cc2CC[N+]1(C)C)OC)O3)OC)OC)OC

  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
NPO8212 Ligularia nelumbifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[12088436]
NPO25510 Plectranthus ernstii Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19445517]
NPO8212 Ligularia nelumbifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22472691]
NPO28026 Grifola frondosa Species Schizophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO435 Bohadschia marmorata Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO595 Tephrosia falciformis Species Geometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8077 Artocarpus incisa Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25510 Plectranthus ernstii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8212 Ligularia nelumbifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1114 Cetraria australiensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28026 Grifola frondosa Species Schizophyllaceae Eukaryota n.a. n.a. Database[FooDB]
NPO859 Berberis oblonga Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO859 Berberis oblonga Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8212 Ligularia nelumbifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8077 Artocarpus incisa Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO435 Bohadschia marmorata Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25510 Plectranthus ernstii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8077 Artocarpus incisa Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8212 Ligularia nelumbifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO595 Tephrosia falciformis Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10518 Chrysanthemum myconis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1114 Cetraria australiensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO859 Berberis oblonga Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28026 Grifola frondosa Species Schizophyllaceae 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 NPC256213 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
0.7619 Intermediate Similarity NPC10871
0.7051 Intermediate Similarity NPC76682
0.7051 Intermediate Similarity NPC10908
0.7051 Intermediate Similarity NPC63646
0.7051 Intermediate Similarity NPC317145
0.7051 Intermediate Similarity NPC198498
0.7051 Intermediate Similarity NPC115284
0.6962 Remote Similarity NPC276890
0.6463 Remote Similarity NPC227060
0.6351 Remote Similarity NPC317439
0.6235 Remote Similarity NPC73492
0.6235 Remote Similarity NPC299990
0.6235 Remote Similarity NPC480587
0.6145 Remote Similarity NPC41376
0.6023 Remote Similarity NPC185639
0.6023 Remote Similarity NPC251735
0.6023 Remote Similarity NPC49075
0.6023 Remote Similarity NPC599951
0.6 Remote Similarity NPC12424
0.6 Remote Similarity NPC129518
0.6 Remote Similarity NPC251580
0.5934 Remote Similarity NPC475479
0.5934 Remote Similarity NPC323537
0.593 Remote Similarity NPC603853
0.5909 Remote Similarity NPC311973
0.587 Remote Similarity NPC485712
0.5862 Remote Similarity NPC290582
0.5862 Remote Similarity NPC217748
0.5862 Remote Similarity NPC182052
0.5862 Remote Similarity NPC271013
0.5862 Remote Similarity NPC42663
0.5862 Remote Similarity NPC15414
0.5843 Remote Similarity NPC116465
0.5843 Remote Similarity NPC223690
0.5843 Remote Similarity NPC9532
0.5795 Remote Similarity NPC279228
0.5778 Remote Similarity NPC229373
0.5696 Remote Similarity NPC247639
0.5696 Remote Similarity NPC25084
0.5556 Remote Similarity NPC239824
0.5532 Remote Similarity NPC249996
0.5495 Remote Similarity NPC254441
0.5484 Remote Similarity NPC195538
0.5368 Remote Similarity NPC24260
0.5361 Remote Similarity NPC480586
0.5361 Remote Similarity NPC480590
0.5306 Remote Similarity NPC281581
0.5253 Remote Similarity NPC485711
0.5169 Remote Similarity NPC603603
0.5158 Remote Similarity NPC16357
0.5158 Remote Similarity NPC302245
0.5122 Remote Similarity NPC104196
0.5104 Remote Similarity NPC212237
0.5104 Remote Similarity NPC243454
0.5053 Remote Similarity NPC181796
0.5053 Remote Similarity NPC290005
0.5053 Remote Similarity NPC54654
0.5053 Remote Similarity NPC7715
0.5053 Remote Similarity NPC328155
0.5053 Remote Similarity NPC222661
0.5053 Remote Similarity NPC285931
0.5052 Remote Similarity NPC611658

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC256213 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
0.7051 Intermediate Similarity NPD8099 Discontinued
0.6506 Remote Similarity NPD8156 Discontinued
0.642 Remote Similarity NPD8252 Phase 4
0.6341 Remote Similarity NPD8251 Approved
0.5862 Remote Similarity NPD8095 Phase 1
0.5556 Remote Similarity NPD8053 Approved
0.55 Remote Similarity NPD8054 Phase 4

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