Natural Product: NPC485736

Natural Product IDNPC485736
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FDFRQMKAXPLXFL-UZAJRZOCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 171263
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002875] Tigliane and ingenane diterpenoids
            • [CHEMONTID:0002906] Phorbol esters

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 FDFRQMKAXPLXFL-UZAJRZOCSA-N
Standard InCHI InChI=1S/C34H54O6/c1-6-7-8-9-10-11-12-13-14-15-16-17-28(36)40-33-20-24(3)34(39)26(29(33)31(33,4)5)19-25(22-35)21-32(38)27(34)18-23(2)30(32)37/h18-19,24,26-27,29,35,38-39H,6-17,20-22H2,1-5H3/t24-,26+,27-,29-,32-,33+,34-/m1/s1
SMILES CCCCCCCCCCCCCC(=O)O[C@@]12C[C@@H](C)[C@]3([C@@H](C=C(C[C@]4([C@H]3C=C(C)C4=O)O)CO)[C@@H]1C2(C)C)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
NPO40934 Stillingia loranthacea Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[31599155]

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
NPT189 Cell line Vero Chlorocebus aethiops CC50 = 24600.0 nM PMID[31599155]

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 NPC485736 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
1.0 High Similarity NPC277477
1.0 High Similarity NPC479003
1.0 High Similarity NPC485735
0.8889 High Similarity NPC485732
0.8136 Intermediate Similarity NPC153036
0.8095 Intermediate Similarity NPC485733
0.7869 Intermediate Similarity NPC158523
0.7846 Intermediate Similarity NPC482454
0.7727 Intermediate Similarity NPC17138
0.7727 Intermediate Similarity NPC101825
0.7727 Intermediate Similarity NPC215643
0.7727 Intermediate Similarity NPC265499
0.7619 Intermediate Similarity NPC71889
0.7619 Intermediate Similarity NPC475937
0.7612 Intermediate Similarity NPC221511
0.7286 Intermediate Similarity NPC151216
0.7286 Intermediate Similarity NPC89227
0.7246 Intermediate Similarity NPC485731
0.7206 Intermediate Similarity NPC170212
0.7123 Intermediate Similarity NPC472760
0.7 Intermediate Similarity NPC477091
0.6957 Remote Similarity NPC275696
0.6957 Remote Similarity NPC255081
0.6712 Remote Similarity NPC479000
0.6667 Remote Similarity NPC153651
0.662 Remote Similarity NPC5991
0.662 Remote Similarity NPC196500
0.662 Remote Similarity NPC471108
0.662 Remote Similarity NPC5989
0.6575 Remote Similarity NPC22628
0.6575 Remote Similarity NPC600005
0.6462 Remote Similarity NPC91189
0.6269 Remote Similarity NPC96739
0.6197 Remote Similarity NPC609113
0.6143 Remote Similarity NPC171905
0.6 Remote Similarity NPC174471
0.5974 Remote Similarity NPC609983
0.5946 Remote Similarity NPC474872
0.5926 Remote Similarity NPC180640
0.5867 Remote Similarity NPC603912
0.5854 Remote Similarity NPC185876
0.5854 Remote Similarity NPC19336
0.5833 Remote Similarity NPC474871
0.5833 Remote Similarity NPC260786
0.5802 Remote Similarity NPC138641
0.5802 Remote Similarity NPC611243
0.5652 Remote Similarity NPC156252
0.5641 Remote Similarity NPC484333
0.5513 Remote Similarity NPC183540
0.5479 Remote Similarity NPC472397
0.5432 Remote Similarity NPC159692
0.5333 Remote Similarity NPC157252
0.5333 Remote Similarity NPC472758
0.5309 Remote Similarity NPC222307
0.5301 Remote Similarity NPC469647
0.5301 Remote Similarity NPC469648
0.527 Remote Similarity NPC478681
0.5263 Remote Similarity NPC471125
0.5195 Remote Similarity NPC145182
0.5122 Remote Similarity NPC602538
0.5119 Remote Similarity NPC482199
0.5119 Remote Similarity NPC482197
0.5116 Remote Similarity NPC479001
0.5116 Remote Similarity NPC479002
0.5114 Remote Similarity NPC283875
0.5063 Remote Similarity NPC471128
0.5063 Remote Similarity NPC471126

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485736 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