Natural Product: NPC100451

Natural Product IDNPC100451
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CZCROZIJKBXZDP-IKEOEMBBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101952
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 CZCROZIJKBXZDP-IKEOEMBBSA-N
Standard InCHI InChI=1S/C29H44O4/c1-17-8-13-29(31-16-17)18(2)26-25(33-29)15-24-22-7-6-20-14-21(32-19(3)30)9-11-27(20,4)23(22)10-12-28(24,26)5/h6,17-18,21-26H,7-16H2,1-5H3/t17-,18+,21+,22-,23+,24+,25+,26+,27+,28+,29-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)OC(=O)C)O2)OC1

  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
NPO40499 Dioscorea nipponica Makino subsp. rosthornii (Prain et Burkill) C. T. Ting Strain Dioscoreaceae Eukaryota Rhizomes n.a. n.a. PMID[28606759]
NPO40499 Dioscorea nipponica Makino subsp. rosthornii (Prain et Burkill) C. T. Ting Strain Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT397 Cell line NCI-H460 Homo sapiens IC50 > 50000.0 nM PMID[28606759]

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 NPC100451 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
0.7143 Intermediate Similarity NPC235126
0.7143 Intermediate Similarity NPC242419
0.6962 Remote Similarity NPC181845
0.6667 Remote Similarity NPC470613
0.6667 Remote Similarity NPC470612
0.6267 Remote Similarity NPC486119
0.625 Remote Similarity NPC470432
0.625 Remote Similarity NPC230507
0.625 Remote Similarity NPC187159
0.6111 Remote Similarity NPC113044
0.6111 Remote Similarity NPC283829
0.6111 Remote Similarity NPC14704
0.6111 Remote Similarity NPC161676
0.5921 Remote Similarity NPC177818
0.5914 Remote Similarity NPC470433
0.5914 Remote Similarity NPC46190
0.5914 Remote Similarity NPC171073
0.5914 Remote Similarity NPC602423
0.5851 Remote Similarity NPC477809
0.5789 Remote Similarity NPC300557
0.5769 Remote Similarity NPC485606
0.5729 Remote Similarity NPC480555
0.5729 Remote Similarity NPC150372
0.5714 Remote Similarity NPC469599
0.5657 Remote Similarity NPC475333
0.5657 Remote Similarity NPC224098
0.5657 Remote Similarity NPC208383
0.5556 Remote Similarity NPC269297
0.5556 Remote Similarity NPC222202
0.5514 Remote Similarity NPC477808
0.5493 Remote Similarity NPC153987
0.5464 Remote Similarity NPC6806
0.5417 Remote Similarity NPC44083
0.5392 Remote Similarity NPC480554
0.5362 Remote Similarity NPC609635
0.5361 Remote Similarity NPC248746
0.5342 Remote Similarity NPC24556
0.5288 Remote Similarity NPC480553
0.5288 Remote Similarity NPC477811
0.5248 Remote Similarity NPC475550
0.5196 Remote Similarity NPC309278
0.5195 Remote Similarity NPC305808
0.5185 Remote Similarity NPC480556
0.5146 Remote Similarity NPC194207
0.5146 Remote Similarity NPC22779
0.5138 Remote Similarity NPC224314
0.5067 Remote Similarity NPC248944
0.5067 Remote Similarity NPC7479
0.5067 Remote Similarity NPC257296

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC100451 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
0.5067 Remote Similarity NPD6928 Phase 2

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