Natural Product: NPC609415

Natural Product IDNPC609415
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MECGDTAEMVIQNQ-QBDOPFNQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL245073
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 MECGDTAEMVIQNQ-QBDOPFNQSA-N
Standard InCHI InChI=1S/C37H70O4/c1-3-4-5-6-7-8-9-10-11-15-18-21-24-27-30-35(38)36(39)31-28-25-22-19-16-13-12-14-17-20-23-26-29-34-32-33(2)41-37(34)40/h32-33,35-36,38-39H,3-31H2,1-2H3/t33-,35-,36-/m0/s1
SMILES CCCCCCCCCCCCCCCC[C@H](O)[C@@H](O)CCCCCCCCCCCCCCC1=C[C@H](C)OC1=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
NPO63220 Uvaria tonkinesis Genus Annonaceae 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
NPT28438 Unchecked Unchecked n.a. IC50 = 580.0 nM PMID[17321744]

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 NPC609415 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
0.825 Intermediate Similarity NPC329829
0.75 Intermediate Similarity NPC219652
0.75 Intermediate Similarity NPC473840
0.75 Intermediate Similarity NPC73310
0.75 Intermediate Similarity NPC473529
0.75 Intermediate Similarity NPC180363
0.75 Intermediate Similarity NPC94875
0.75 Intermediate Similarity NPC11332
0.75 Intermediate Similarity NPC145914
0.75 Intermediate Similarity NPC601174
0.75 Intermediate Similarity NPC601403
0.75 Intermediate Similarity NPC603568
0.75 Intermediate Similarity NPC604330
0.75 Intermediate Similarity NPC608300
0.75 Intermediate Similarity NPC611200
0.75 Intermediate Similarity NPC611571
0.7333 Intermediate Similarity NPC65930
0.7174 Intermediate Similarity NPC329838
0.7174 Intermediate Similarity NPC329615
0.7174 Intermediate Similarity NPC600188
0.7111 Intermediate Similarity NPC25703
0.6977 Remote Similarity NPC25764
0.6977 Remote Similarity NPC235809
0.6977 Remote Similarity NPC39279
0.6977 Remote Similarity NPC475159
0.6977 Remote Similarity NPC39167
0.6977 Remote Similarity NPC131002
0.6977 Remote Similarity NPC292809
0.6977 Remote Similarity NPC202055
0.6977 Remote Similarity NPC473780
0.6977 Remote Similarity NPC604521
0.6977 Remote Similarity NPC606804
0.6977 Remote Similarity NPC607425
0.6977 Remote Similarity NPC608574
0.697 Remote Similarity NPC84038
0.6889 Remote Similarity NPC600524
0.6889 Remote Similarity NPC608355
0.6809 Remote Similarity NPC485250
0.6735 Remote Similarity NPC480082
0.6667 Remote Similarity NPC156804
0.6522 Remote Similarity NPC473156
0.6522 Remote Similarity NPC163093
0.6522 Remote Similarity NPC144415
0.6522 Remote Similarity NPC282815
0.6522 Remote Similarity NPC600956
0.6522 Remote Similarity NPC607439
0.6522 Remote Similarity NPC608157
0.65 Remote Similarity NPC608138
0.6383 Remote Similarity NPC473671
0.6383 Remote Similarity NPC475268
0.6383 Remote Similarity NPC470400
0.6383 Remote Similarity NPC77871
0.6383 Remote Similarity NPC9678
0.6383 Remote Similarity NPC241360
0.6383 Remote Similarity NPC293136
0.6383 Remote Similarity NPC319036
0.6383 Remote Similarity NPC605867
0.6346 Remote Similarity NPC473905
0.6346 Remote Similarity NPC253801
0.6327 Remote Similarity NPC477012
0.625 Remote Similarity NPC132940
0.6222 Remote Similarity NPC100921
0.6222 Remote Similarity NPC477018
0.617 Remote Similarity NPC134865
0.617 Remote Similarity NPC488246
0.617 Remote Similarity NPC103523
0.617 Remote Similarity NPC488627
0.617 Remote Similarity NPC480080
0.617 Remote Similarity NPC488631
0.617 Remote Similarity NPC477011
0.617 Remote Similarity NPC610454
0.6122 Remote Similarity NPC20533
0.6122 Remote Similarity NPC605396
0.6078 Remote Similarity NPC320458
0.6053 Remote Similarity NPC218477
0.6053 Remote Similarity NPC474705
0.6053 Remote Similarity NPC186531
0.6042 Remote Similarity NPC480079
0.5882 Remote Similarity NPC120398
0.5882 Remote Similarity NPC258068
0.5882 Remote Similarity NPC473995
0.5882 Remote Similarity NPC471567
0.5882 Remote Similarity NPC476583
0.5849 Remote Similarity NPC322529
0.5833 Remote Similarity NPC473649
0.5833 Remote Similarity NPC154097
0.5833 Remote Similarity NPC159750
0.5833 Remote Similarity NPC73248
0.5833 Remote Similarity NPC470401
0.5769 Remote Similarity NPC477014
0.5769 Remote Similarity NPC477013
0.5714 Remote Similarity NPC604764
0.5686 Remote Similarity NPC473478
0.5686 Remote Similarity NPC473651
0.5686 Remote Similarity NPC66346
0.5652 Remote Similarity NPC606043
0.5577 Remote Similarity NPC231096
0.5577 Remote Similarity NPC475581
0.5577 Remote Similarity NPC283085
0.5577 Remote Similarity NPC62118
0.5577 Remote Similarity NPC132496
0.5577 Remote Similarity NPC107717
0.5577 Remote Similarity NPC488252
0.5577 Remote Similarity NPC488244
0.5577 Remote Similarity NPC606740
0.5577 Remote Similarity NPC608614
0.5556 Remote Similarity NPC473520
0.5556 Remote Similarity NPC280612
0.5532 Remote Similarity NPC107986
0.5532 Remote Similarity NPC223871
0.5532 Remote Similarity NPC231009
0.5532 Remote Similarity NPC103284
0.5532 Remote Similarity NPC110710
0.5532 Remote Similarity NPC1083
0.5532 Remote Similarity NPC82795
0.5532 Remote Similarity NPC286338
0.5532 Remote Similarity NPC603931
0.5532 Remote Similarity NPC604237
0.549 Remote Similarity NPC309211
0.549 Remote Similarity NPC477010
0.5472 Remote Similarity NPC233551
0.5472 Remote Similarity NPC40376
0.5472 Remote Similarity NPC21208
0.5455 Remote Similarity NPC477015
0.5435 Remote Similarity NPC112685
0.5417 Remote Similarity NPC488253
0.5417 Remote Similarity NPC473669
0.5417 Remote Similarity NPC488251
0.5306 Remote Similarity NPC81045
0.5306 Remote Similarity NPC232555
0.5306 Remote Similarity NPC39754
0.5306 Remote Similarity NPC171135
0.5306 Remote Similarity NPC171174
0.5306 Remote Similarity NPC182383
0.5306 Remote Similarity NPC114694
0.5306 Remote Similarity NPC61257
0.5306 Remote Similarity NPC320569
0.5306 Remote Similarity NPC485248
0.5306 Remote Similarity NPC133730
0.5306 Remote Similarity NPC191929
0.5306 Remote Similarity NPC142117
0.5306 Remote Similarity NPC100454
0.5306 Remote Similarity NPC242364
0.5306 Remote Similarity NPC480249
0.5306 Remote Similarity NPC172821
0.5306 Remote Similarity NPC485249
0.5306 Remote Similarity NPC274446
0.5306 Remote Similarity NPC485251
0.5306 Remote Similarity NPC151403
0.5306 Remote Similarity NPC240695
0.5306 Remote Similarity NPC261952
0.5306 Remote Similarity NPC605171
0.5273 Remote Similarity NPC91067
0.5273 Remote Similarity NPC480081
0.52 Remote Similarity NPC93794
0.52 Remote Similarity NPC488632
0.52 Remote Similarity NPC473504
0.52 Remote Similarity NPC81778
0.52 Remote Similarity NPC40066
0.52 Remote Similarity NPC47937
0.5185 Remote Similarity NPC89001
0.5098 Remote Similarity NPC280621
0.5098 Remote Similarity NPC48338
0.5098 Remote Similarity NPC488628

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC609415 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