Natural Product: NPC483885

Natural Product IDNPC483885
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.
 IFGBTIWEAAHLBD-IVZQPQJMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44361908
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 IFGBTIWEAAHLBD-IVZQPQJMSA-N
Standard InCHI InChI=1S/C39H41NO12/c1-23(41)47-22-38-30(50-33(43)25-13-8-6-9-14-25)19-28-31(51-34(44)26-15-10-7-11-16-26)39(38,52-36(28,3)4)37(5,46)20-29(32(38)48-24(2)42)49-35(45)27-17-12-18-40-21-27/h6-18,21,28-32,46H,19-20,22H2,1-5H3/t28?,29-,30+,31-,32+,37+,38-,39?/m1/s1
SMILES CC(=O)OC[C@@]12[C@H](CC3[C@H](C2([C@](C)(C[C@H]([C@@H]1OC(=O)C)OC(=O)c1cccnc1)O)OC3(C)C)OC(=O)c1ccccc1)OC(=O)c1ccccc1

  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 = 45.0 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 94.8 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 25.8 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 91.3 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 8.2 % PMID[11741484]
NPT2 Others Unspecified n.a. Inhibition = 80.7 % 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 NPC483885 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
0.8987 High Similarity NPC176413
0.8519 High Similarity NPC294512
0.8072 Intermediate Similarity NPC479045
0.7922 Intermediate Similarity NPC70716
0.7922 Intermediate Similarity NPC95265
0.759 Intermediate Similarity NPC75600
0.759 Intermediate Similarity NPC483884
0.7558 Intermediate Similarity NPC483868
0.7531 Intermediate Similarity NPC6815
0.7468 Intermediate Similarity NPC97667
0.7262 Intermediate Similarity NPC56953
0.7108 Intermediate Similarity NPC479049
0.7073 Intermediate Similarity NPC479042
0.7059 Intermediate Similarity NPC479041
0.686 Remote Similarity NPC610134
0.6627 Remote Similarity NPC127720
0.6552 Remote Similarity NPC479048
0.6404 Remote Similarity NPC483870
0.6279 Remote Similarity NPC609309
0.6265 Remote Similarity NPC171207
0.6264 Remote Similarity NPC483869
0.6235 Remote Similarity NPC96903
0.6222 Remote Similarity NPC127026
0.6222 Remote Similarity NPC483890
0.618 Remote Similarity NPC610927
0.6118 Remote Similarity NPC472569
0.6024 Remote Similarity NPC191082
0.5977 Remote Similarity NPC472568
0.593 Remote Similarity NPC472570
0.5876 Remote Similarity NPC471980
0.587 Remote Similarity NPC10904
0.587 Remote Similarity NPC148896
0.5843 Remote Similarity NPC481488
0.5833 Remote Similarity NPC4341
0.5824 Remote Similarity NPC611111
0.5761 Remote Similarity NPC301368
0.5761 Remote Similarity NPC84815
0.5747 Remote Similarity NPC11685
0.5747 Remote Similarity NPC16912
0.5699 Remote Similarity NPC180668
0.5647 Remote Similarity NPC479047
0.5647 Remote Similarity NPC291638
0.5618 Remote Similarity NPC471102
0.5612 Remote Similarity NPC471013
0.56 Remote Similarity NPC6981
0.5581 Remote Similarity NPC67777
0.5568 Remote Similarity NPC57628
0.5556 Remote Similarity NPC481489
0.5426 Remote Similarity NPC473089
0.5402 Remote Similarity NPC139067
0.5402 Remote Similarity NPC177340
0.5392 Remote Similarity NPC483880
0.5392 Remote Similarity NPC156941
0.5333 Remote Similarity NPC184747
0.5281 Remote Similarity NPC479044
0.5275 Remote Similarity NPC282239
0.5227 Remote Similarity NPC270590
0.5227 Remote Similarity NPC43241
0.5217 Remote Similarity NPC294803
0.5161 Remote Similarity NPC483887
0.5161 Remote Similarity NPC158020
0.5111 Remote Similarity NPC41481
0.5106 Remote Similarity NPC608007
0.5054 Remote Similarity NPC481064
0.5054 Remote Similarity NPC481062
0.5054 Remote Similarity NPC481058
0.5054 Remote Similarity NPC481060
0.5053 Remote Similarity NPC483889
0.5051 Remote Similarity NPC30171
0.505 Remote Similarity NPC96801
0.505 Remote Similarity NPC150698
0.5049 Remote Similarity NPC294579
0.5049 Remote Similarity NPC144779

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC483885 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