Natural Product: NPC483886

Natural Product IDNPC483886
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PXDXQOQNFDIAAF-ZITBYFKDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44361909
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

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 PXDXQOQNFDIAAF-ZITBYFKDSA-N
Standard InCHI InChI=1S/C40H42O12/c1-23(41)47-30-29-32(48-24(2)42)40(52-37(29,3)4)38(5,46)22-28(49-34(43)25-16-10-7-11-17-25)31(50-35(44)26-18-12-8-13-19-26)39(40,6)33(30)51-36(45)27-20-14-9-15-21-27/h7-21,28-33,46H,22H2,1-6H3/t28-,29?,30+,31+,32-,33+,38+,39+,40?/m1/s1
SMILES CC(=O)O[C@H]1C2[C@H](C3([C@](C)(C[C@H]([C@@H]([C@@]3(C)[C@H]1OC(=O)c1ccccc1)OC(=O)c1ccccc1)OC(=O)c1ccccc1)O)OC2(C)C)OC(=O)C

  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
NPO3859 Maytenus magellanica Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11741484]
NPO10966 Maytenus chubutensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11741484]
NPO10966 Maytenus chubutensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3859 Maytenus magellanica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10966 Maytenus chubutensis Species Celastraceae 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
NPT2 Others Unspecified n.a. Inhibition = 16.2 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 92.0 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 19.7 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 82.2 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 9.7 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 60.3 % PMID[11741484]

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 NPC483886 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
0.8689 High Similarity NPC281717
0.7761 Intermediate Similarity NPC472569
0.7324 Intermediate Similarity NPC481488
0.7246 Intermediate Similarity NPC16912
0.7059 Intermediate Similarity NPC471101
0.7013 Intermediate Similarity NPC30171
0.6957 Remote Similarity NPC471104
0.6944 Remote Similarity NPC481489
0.6912 Remote Similarity NPC163719
0.6912 Remote Similarity NPC200471
0.6912 Remote Similarity NPC95810
0.6912 Remote Similarity NPC472575
0.6761 Remote Similarity NPC11685
0.6761 Remote Similarity NPC472570
0.6571 Remote Similarity NPC472572
0.6301 Remote Similarity NPC57628
0.6154 Remote Similarity NPC125106
0.6154 Remote Similarity NPC472573
0.6087 Remote Similarity NPC481047
0.6087 Remote Similarity NPC481045
0.6076 Remote Similarity NPC301368
0.6076 Remote Similarity NPC84815
0.6 Remote Similarity NPC70716
0.5974 Remote Similarity NPC481486
0.5921 Remote Similarity NPC471102
0.5915 Remote Similarity NPC483862
0.5857 Remote Similarity NPC66761
0.5857 Remote Similarity NPC483843
0.5857 Remote Similarity NPC476094
0.5769 Remote Similarity NPC483887
0.5769 Remote Similarity NPC158020
0.575 Remote Similarity NPC610927
0.5714 Remote Similarity NPC472568
0.5694 Remote Similarity NPC90614
0.5679 Remote Similarity NPC56953
0.5663 Remote Similarity NPC253738
0.561 Remote Similarity NPC483870
0.5584 Remote Similarity NPC97667
0.5513 Remote Similarity NPC282239
0.5479 Remote Similarity NPC483879
0.5467 Remote Similarity NPC158663
0.5443 Remote Similarity NPC479042
0.5417 Remote Similarity NPC475429
0.5417 Remote Similarity NPC211137
0.5405 Remote Similarity NPC473060
0.5385 Remote Similarity NPC95265
0.5349 Remote Similarity NPC479045
0.5333 Remote Similarity NPC472576
0.527 Remote Similarity NPC152440
0.527 Remote Similarity NPC241951
0.527 Remote Similarity NPC483888
0.5263 Remote Similarity NPC270590
0.5256 Remote Similarity NPC479043
0.5256 Remote Similarity NPC609924
0.525 Remote Similarity NPC481050
0.52 Remote Similarity NPC51314
0.52 Remote Similarity NPC87448
0.5132 Remote Similarity NPC291599
0.5132 Remote Similarity NPC90257
0.5132 Remote Similarity NPC69357
0.5125 Remote Similarity NPC481490
0.5122 Remote Similarity NPC488917
0.5122 Remote Similarity NPC603877
0.5122 Remote Similarity NPC608007
0.5116 Remote Similarity NPC483869
0.5067 Remote Similarity NPC483882
0.5065 Remote Similarity NPC147217
0.5065 Remote Similarity NPC137718
0.5062 Remote Similarity NPC609221
0.5059 Remote Similarity NPC483864

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC483886 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