Natural Product: NPC38977

Natural Product IDNPC38977
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WMLUIAYRBBKAJC-KYJUHHDHSA-O
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14753650
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 WMLUIAYRBBKAJC-KYJUHHDHSA-O
Standard InCHI InChI=1S/C38H42N2O6/c1-39-15-13-25-20-32(43-5)34-22-28(25)29(39)17-23-7-10-27(11-8-23)45-33-19-24(9-12-31(33)42-4)18-30-36-26(14-16-40(30,2)3)21-35(44-6)37(41)38(36)46-34/h7-12,19-22,29-30H,13-18H2,1-6H3/p+1/t29-,30-/m0/s1
SMILES CN1CCc2cc(c3cc2[C@@H]1Cc1ccc(cc1)Oc1cc(ccc1OC)C[C@H]1c2c(CC[N+]1(C)C)cc(c(c2O3)O)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
NPO1179 Anaxagorea luzonensis Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10959592]
NPO755 Phoradendron reichenbachianum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[11488459]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. root n.a. PMID[20030508]
NPO3148 Melianthus major Species Melianthaceae Eukaryota Leaves n.a. n.a. PMID[32663024]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[3728032]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[38868673]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[38999684]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO2679 Dictyota bartayresiana Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11802 Physeter catodon Species Physeteridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12183 Argyreia nervosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28111 Lathyrus aphaca Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3148 Melianthus major Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5783 Acronychia muelleri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12183 Argyreia nervosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11802 Physeter catodon Species Physeteridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12183 Argyreia nervosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11802 Physeter catodon Species Physeteridae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12183 Argyreia nervosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11802 Physeter catodon Species Physeteridae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21826 Vulpicida juniperinus Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28111 Lathyrus aphaca Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3148 Melianthus major Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5377 Tapinoma erraticum Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO755 Phoradendron reichenbachianum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12882 Clitocybe fasciculata Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1179 Anaxagorea luzonensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12430 Erythrina chiriquensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18003 Leptolyngbya lurida Species Leptolyngbyaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2679 Dictyota bartayresiana Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11802 Physeter catodon Species Physeteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22389 Phelipanche arenaria Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12183 Argyreia nervosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5783 Acronychia muelleri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15367 Croton regelianus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12663 Penicillium implicatum Species Aspergillaceae 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 NPC38977 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
0.7108 Intermediate Similarity NPC290582
0.7108 Intermediate Similarity NPC217748
0.7108 Intermediate Similarity NPC182052
0.7108 Intermediate Similarity NPC271013
0.7108 Intermediate Similarity NPC42663
0.7108 Intermediate Similarity NPC15414
0.6824 Remote Similarity NPC279228
0.6211 Remote Similarity NPC82457
0.6163 Remote Similarity NPC603603
0.6154 Remote Similarity NPC181796
0.6154 Remote Similarity NPC54654
0.6154 Remote Similarity NPC7715
0.6154 Remote Similarity NPC328155
0.6154 Remote Similarity NPC222661
0.6154 Remote Similarity NPC285931
0.6044 Remote Similarity NPC216252
0.6 Remote Similarity NPC247639
0.6 Remote Similarity NPC311973
0.6 Remote Similarity NPC25084
0.5978 Remote Similarity NPC290005
0.5824 Remote Similarity NPC239824
0.5761 Remote Similarity NPC116465
0.5747 Remote Similarity NPC76682
0.5747 Remote Similarity NPC10908
0.5747 Remote Similarity NPC63646
0.5747 Remote Similarity NPC317145
0.5747 Remote Similarity NPC198498
0.5747 Remote Similarity NPC115284
0.5699 Remote Similarity NPC229373
0.5591 Remote Similarity NPC254441
0.5556 Remote Similarity NPC11296
0.5556 Remote Similarity NPC274661
0.5506 Remote Similarity NPC276890
0.5495 Remote Similarity NPC603853
0.5484 Remote Similarity NPC286119
0.5464 Remote Similarity NPC275680
0.5464 Remote Similarity NPC22115
0.5435 Remote Similarity NPC73492
0.5435 Remote Similarity NPC299990
0.5422 Remote Similarity NPC104196
0.5385 Remote Similarity NPC12424
0.5385 Remote Similarity NPC129518
0.5385 Remote Similarity NPC251580
0.5269 Remote Similarity NPC480587
0.5263 Remote Similarity NPC185639
0.5263 Remote Similarity NPC251735
0.5263 Remote Similarity NPC49075
0.5263 Remote Similarity NPC223690
0.5263 Remote Similarity NPC9532
0.5263 Remote Similarity NPC599951
0.5258 Remote Similarity NPC195538
0.5227 Remote Similarity NPC30779
0.5149 Remote Similarity NPC480586
0.5143 Remote Similarity NPC90998
0.5114 Remote Similarity NPC317272
0.5114 Remote Similarity NPC268503
0.5111 Remote Similarity NPC256012
0.5111 Remote Similarity NPC610965
0.5055 Remote Similarity NPC480592
0.5054 Remote Similarity NPC240841
0.5054 Remote Similarity NPC610959
0.5051 Remote Similarity NPC212237
0.5051 Remote Similarity NPC243454
0.5048 Remote Similarity NPC48490

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC38977 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
0.8488 Intermediate Similarity NPD8054 Phase 4
0.6989 Remote Similarity NPD8053 Approved
0.5747 Remote Similarity NPD8099 Discontinued
0.5667 Remote Similarity NPD8156 Discontinued
0.5435 Remote Similarity NPD8095 Phase 1
0.5393 Remote Similarity NPD8252 Phase 4
0.5333 Remote Similarity NPD8251 Approved

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