Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC248627

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT567 Individual Protein Matrix metalloproteinase 3 Homo sapiens Inhibition = 7.0 % PMID[502554]
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Inhibition = 8.0 % PMID[502554]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus Inhibition = 8.0 % PMID[502554]
NPT280 Individual Protein Matrix metalloproteinase 9 Homo sapiens Inhibition = 1.0 % PMID[502554]
NPT568 Individual Protein Matrix metalloproteinase-2 Homo sapiens Inhibition = -7.0 % PMID[502554]
NPT569 Individual Protein Matrix metalloproteinase 8 Homo sapiens Inhibition = 11.0 % PMID[502554]
NPT570 Individual Protein Arachidonate 5-lipoxygenase Homo sapiens Inhibition = 24.0 % PMID[502554]
NPT43 Individual Protein Tyrosinase Agaricus bisporus Inhibition = -4.0 % PMID[502554]
NPT69 Individual Protein Matrix metalloproteinase-1 Homo sapiens Inhibition = 13.0 % PMID[502554]
NPT947 Individual Protein Carbonic anhydrase I Homo sapiens Ki = 57760.0 nM PMID[502555]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC248627 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7879 Intermediate Similarity NPC260919
0.7373 Intermediate Similarity NPC27699
0.6933 Remote Similarity NPC224632
0.6917 Remote Similarity NPC163105
0.6897 Remote Similarity NPC314440
0.6897 Remote Similarity NPC118135
0.6753 Remote Similarity NPC278874
0.6667 Remote Similarity NPC105758
0.6667 Remote Similarity NPC476688
0.6667 Remote Similarity NPC476686
0.6667 Remote Similarity NPC75844
0.6603 Remote Similarity NPC164664
0.656 Remote Similarity NPC329046
0.6519 Remote Similarity NPC208060
0.6481 Remote Similarity NPC144114
0.638 Remote Similarity NPC477891
0.6194 Remote Similarity NPC139776
0.6154 Remote Similarity NPC230805
0.6092 Remote Similarity NPC208751
0.6059 Remote Similarity NPC472289
0.6058 Remote Similarity NPC248007
0.5932 Remote Similarity NPC326364
0.5912 Remote Similarity NPC5707
0.5814 Remote Similarity NPC254762
0.5736 Remote Similarity NPC222061
0.5734 Remote Similarity NPC287876
0.5726 Remote Similarity NPC476128
0.5664 Remote Similarity NPC14330

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC248627 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.84 Intermediate Similarity NPD9187 Approved
0.7879 Intermediate Similarity NPD8825 Phase 2
0.7879 Intermediate Similarity NPD59 Approved
0.7576 Intermediate Similarity NPD533 Approved
0.7373 Intermediate Similarity NPD8571 Phase 3
0.7239 Intermediate Similarity NPD9550 Approved
0.7239 Intermediate Similarity NPD9551 Approved
0.6887 Remote Similarity NPD444 Approved
0.6667 Remote Similarity NPD8566 Approved
0.6532 Remote Similarity NPD9071 Phase 3
0.6389 Remote Similarity NPD852 Discontinued
0.6387 Remote Similarity NPD4143 Clinical (unspecified phase)
0.6204 Remote Similarity NPD9366 Approved
0.6154 Remote Similarity NPD9714 Clinical (unspecified phase)
0.6148 Remote Similarity NPD306 Approved
0.6058 Remote Similarity NPD9084 Phase 2
0.5912 Remote Similarity NPD8830 Phase 3
0.5833 Remote Similarity NPD9083 Clinical (unspecified phase)
0.5763 Remote Similarity NPD6594 Discontinued
0.576 Remote Similarity NPD9194 Approved
0.576 Remote Similarity NPD9193 Approved
0.575 Remote Similarity NPD8565 Clinical (unspecified phase)
0.5734 Remote Similarity NPD8829 Clinical (unspecified phase)
0.5698 Remote Similarity NPD7419 Discontinued
0.5671 Remote Similarity NPD761 Approved
0.5671 Remote Similarity NPD741 Approved
0.5644 Remote Similarity NPD5925 Phase 1

  Bioactivity similarity: Similar Natural Products in NPASS

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