Natural Product: NPC475616

Natural Product IDNPC475616
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2,4-Cis And Trans)-Gigantecinone
IUPAC Name (5R)-5-[5-[(2R,5S)-5-[(1S,4R)-1,4-dihydroxy-4-[(2R,5R)-5-[(1R)-1-hydroxytridecyl]oxolan-2-yl]butyl]oxolan-2-yl]pentyl]-3-(2-oxopropyl)oxolan-2-one
Synonyms (2,4-Cis And Trans)-Gigantecinone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL509358
PubChem CID 10627889
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002518] Annonaceous acetogenins

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 SIKLPUJCNJTZFZ-YUECQCAUSA-N
Standard InCHI InChI=1S/C37H66O8/c1-3-4-5-6-7-8-9-10-11-15-18-31(39)35-23-24-36(45-35)33(41)21-20-32(40)34-22-19-29(43-34)16-13-12-14-17-30-26-28(25-27(2)38)37(42)44-30/h28-36,39-41H,3-26H2,1-2H3/t28?,29-,30-,31-,32+,33-,34+,35-,36-/m1/s1
SMILES CCCCCCCCCCCCC(C1CCC(O1)C(CCC(C2CCC(O2)CCCCCC3CC(C(=O)O3)CC(=O)C)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
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. bark n.a. PMID[1479382]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota bark n.a. n.a. PMID[1479382]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[1791471]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[2614426]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9322367]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9917277]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7202 Goniothalamus giganteus Species Annonaceae 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
NPT81 Cell line A549 Homo sapiens ED50 = 2.14 10'-1 ug/ml PMID[8691207]
NPT83 Cell line MCF7 Homo sapiens ED50 > 1.0 ug ml-1 PMID[10514324]
NPT139 Cell line HT-29 Homo sapiens ED50 > 1.0 ug ml-1 PMID[19928902]
NPT376 Cell line A498 Homo sapiens ED50 = 2.12 10'-1 ug/ml PMID[18663020]
NPT306 Cell line PC-3 Homo sapiens ED50 = 1.08 10'-3 ug/ml PMID[18663020]
NPT783 Cell line MIA PaCa-2 Homo sapiens ED50 > 1.0 ug ml-1 PMID[11421741]

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
- Aedes aegypti LC50 = 0.27 ug.mL-1 PMID[18278870]
- Artemia LC50 = 3.27 ppm PMID[20058933]

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 NPC475616 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
0.9091 High Similarity NPC474100
0.9091 High Similarity NPC475232
0.8542 High Similarity NPC480251
0.8542 High Similarity NPC480250
0.8511 High Similarity NPC482767
0.8511 High Similarity NPC475260
0.8511 High Similarity NPC488621
0.8511 High Similarity NPC473775
0.8511 High Similarity NPC488622
0.8163 Intermediate Similarity NPC473699
0.8163 Intermediate Similarity NPC51249
0.8125 Intermediate Similarity NPC480078
0.8125 Intermediate Similarity NPC480071
0.7593 Intermediate Similarity NPC473791
0.75 Intermediate Similarity NPC480076
0.75 Intermediate Similarity NPC480077
0.7308 Intermediate Similarity NPC480075
0.72 Intermediate Similarity NPC488234
0.7143 Intermediate Similarity NPC475206
0.6071 Remote Similarity NPC20621
0.6071 Remote Similarity NPC318963
0.6071 Remote Similarity NPC605101
0.6 Remote Similarity NPC241360
0.6 Remote Similarity NPC293136
0.5593 Remote Similarity NPC258068
0.5593 Remote Similarity NPC476583
0.5577 Remote Similarity NPC480074
0.5424 Remote Similarity NPC473478
0.5424 Remote Similarity NPC473651
0.5424 Remote Similarity NPC66346
0.537 Remote Similarity NPC480072
0.5345 Remote Similarity NPC65930
0.5333 Remote Similarity NPC231096
0.5333 Remote Similarity NPC475581
0.5333 Remote Similarity NPC283085
0.5333 Remote Similarity NPC62118
0.5333 Remote Similarity NPC132496
0.5333 Remote Similarity NPC107717
0.5333 Remote Similarity NPC488252
0.5254 Remote Similarity NPC329615
0.5082 Remote Similarity NPC169511
0.5082 Remote Similarity NPC287164
0.5082 Remote Similarity NPC234077
0.5082 Remote Similarity NPC606740
0.5082 Remote Similarity NPC608614

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC475616 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