Natural Product: NPC293994

Natural Product IDNPC293994
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BGNFAXBUPZDKDC-CMWLGVBASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 53392996
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 BGNFAXBUPZDKDC-CMWLGVBASA-N
Standard InCHI InChI=1S/C21H20O12/c22-6-15-18(28)19(29)20(30)21(33-15)31-8-3-9(23)16-10(24)5-13(32-14(16)4-8)7-1-11(25)17(27)12(26)2-7/h1-5,15,18-23,25-30H,6H2/t15-,18-,19+,20-,21-/m1/s1
SMILES c1c(cc(c(c1O)O)O)c1cc(=O)c2c(cc(cc2o1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)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
NPO129 Biebersteinia orphanidis Species Biebersteiniaceae Eukaryota n.a. n.a. n.a. PMID[11198823]
NPO129 Biebersteinia orphanidis Species Biebersteiniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO129 Biebersteinia orphanidis Species Biebersteiniaceae 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

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 NPC293994 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
0.8696 High Similarity NPC189142
0.8696 High Similarity NPC77660
0.8551 High Similarity NPC261866
0.8406 Intermediate Similarity NPC473043
0.8028 Intermediate Similarity NPC39360
0.8028 Intermediate Similarity NPC29763
0.8028 Intermediate Similarity NPC210003
0.7917 Intermediate Similarity NPC95090
0.7917 Intermediate Similarity NPC27408
0.7733 Intermediate Similarity NPC22832
0.75 Intermediate Similarity NPC243930
0.75 Intermediate Similarity NPC601144
0.7403 Intermediate Similarity NPC311830
0.7403 Intermediate Similarity NPC607707
0.7297 Intermediate Similarity NPC19709
0.6974 Remote Similarity NPC277205
0.6974 Remote Similarity NPC37919
0.6974 Remote Similarity NPC136042
0.6914 Remote Similarity NPC8856
0.6883 Remote Similarity NPC84362
0.6795 Remote Similarity NPC201292
0.6711 Remote Similarity NPC331652
0.6667 Remote Similarity NPC58716
0.6667 Remote Similarity NPC190003
0.6667 Remote Similarity NPC45638
0.6623 Remote Similarity NPC289667
0.6548 Remote Similarity NPC275454
0.6543 Remote Similarity NPC605784
0.6538 Remote Similarity NPC297987
0.6538 Remote Similarity NPC168822
0.6456 Remote Similarity NPC186807
0.6456 Remote Similarity NPC181712
0.641 Remote Similarity NPC58053
0.641 Remote Similarity NPC143851
0.6395 Remote Similarity NPC115674
0.6375 Remote Similarity NPC27942
0.6351 Remote Similarity NPC191154
0.6329 Remote Similarity NPC323593
0.6329 Remote Similarity NPC203500
0.6296 Remote Similarity NPC285197
0.6279 Remote Similarity NPC210073
0.6267 Remote Similarity NPC134819
0.625 Remote Similarity NPC65711
0.625 Remote Similarity NPC105025
0.6203 Remote Similarity NPC45618
0.6145 Remote Similarity NPC116458
0.6145 Remote Similarity NPC246943
0.6125 Remote Similarity NPC93337
0.6125 Remote Similarity NPC146792
0.6125 Remote Similarity NPC158674
0.6118 Remote Similarity NPC606546
0.6098 Remote Similarity NPC191306
0.6098 Remote Similarity NPC609451
0.6049 Remote Similarity NPC610763
0.6024 Remote Similarity NPC284960
0.6024 Remote Similarity NPC486578
0.6024 Remote Similarity NPC605067
0.6 Remote Similarity NPC19388
0.6 Remote Similarity NPC240431
0.6 Remote Similarity NPC55786
0.6 Remote Similarity NPC229409
0.5952 Remote Similarity NPC88023
0.5952 Remote Similarity NPC309025
0.5952 Remote Similarity NPC602805
0.593 Remote Similarity NPC251417
0.5909 Remote Similarity NPC65003
0.5909 Remote Similarity NPC607513
0.5904 Remote Similarity NPC307938
0.5904 Remote Similarity NPC20505
0.587 Remote Similarity NPC475382
0.5833 Remote Similarity NPC80188
0.5833 Remote Similarity NPC601710
0.5802 Remote Similarity NPC238376
0.5795 Remote Similarity NPC44931
0.5765 Remote Similarity NPC220169
0.5745 Remote Similarity NPC253685
0.573 Remote Similarity NPC22062
0.573 Remote Similarity NPC473634
0.573 Remote Similarity NPC138811
0.5698 Remote Similarity NPC601586
0.5652 Remote Similarity NPC209296
0.5652 Remote Similarity NPC150767
0.5618 Remote Similarity NPC227508
0.561 Remote Similarity NPC110349
0.561 Remote Similarity NPC83283
0.5604 Remote Similarity NPC46202
0.5604 Remote Similarity NPC64425
0.5604 Remote Similarity NPC64051
0.5595 Remote Similarity NPC60966
0.5595 Remote Similarity NPC117260
0.5579 Remote Similarity NPC484301
0.5568 Remote Similarity NPC480463
0.5556 Remote Similarity NPC3583
0.5542 Remote Similarity NPC197896
0.5542 Remote Similarity NPC313163
0.5542 Remote Similarity NPC234739
0.5532 Remote Similarity NPC195257
0.5529 Remote Similarity NPC282169
0.5529 Remote Similarity NPC80140
0.5529 Remote Similarity NPC488071
0.5521 Remote Similarity NPC14187
0.5484 Remote Similarity NPC473623
0.5476 Remote Similarity NPC245014
0.5476 Remote Similarity NPC271692
0.5465 Remote Similarity NPC608742
0.5426 Remote Similarity NPC270675
0.5426 Remote Similarity NPC488089
0.5426 Remote Similarity NPC195685
0.5422 Remote Similarity NPC249281
0.5417 Remote Similarity NPC108406
0.5412 Remote Similarity NPC222936
0.5412 Remote Similarity NPC182045
0.5357 Remote Similarity NPC145038
0.5357 Remote Similarity NPC56077
0.5357 Remote Similarity NPC281131
0.5357 Remote Similarity NPC253662
0.5357 Remote Similarity NPC179950
0.5357 Remote Similarity NPC88789
0.5357 Remote Similarity NPC259152
0.5357 Remote Similarity NPC491374
0.5333 Remote Similarity NPC603300
0.5326 Remote Similarity NPC122809
0.5319 Remote Similarity NPC124155
0.5319 Remote Similarity NPC35119
0.5312 Remote Similarity NPC101636
0.5312 Remote Similarity NPC298171
0.53 Remote Similarity NPC480441
0.5294 Remote Similarity NPC22195
0.5294 Remote Similarity NPC21190
0.5294 Remote Similarity NPC73511
0.5258 Remote Similarity NPC472994
0.5248 Remote Similarity NPC311850
0.5244 Remote Similarity NPC34531
0.5238 Remote Similarity NPC108831
0.5238 Remote Similarity NPC182634
0.5196 Remote Similarity NPC488083
0.5192 Remote Similarity NPC198199
0.5176 Remote Similarity NPC282987
0.5176 Remote Similarity NPC64305
0.5176 Remote Similarity NPC609879
0.5172 Remote Similarity NPC611303
0.5158 Remote Similarity NPC210961
0.5158 Remote Similarity NPC32641
0.5158 Remote Similarity NPC256188
0.5149 Remote Similarity NPC470715
0.5149 Remote Similarity NPC164704
0.5116 Remote Similarity NPC46420
0.5116 Remote Similarity NPC349108
0.5116 Remote Similarity NPC600680
0.5116 Remote Similarity NPC603655
0.5114 Remote Similarity NPC21666
0.5109 Remote Similarity NPC67105
0.5096 Remote Similarity NPC68592
0.5067 Remote Similarity NPC177298
0.5059 Remote Similarity NPC77672
0.5059 Remote Similarity NPC133671
0.5059 Remote Similarity NPC135391
0.5059 Remote Similarity NPC78263
0.5059 Remote Similarity NPC250069
0.5057 Remote Similarity NPC42773
0.5057 Remote Similarity NPC472459
0.5057 Remote Similarity NPC45522
0.5057 Remote Similarity NPC599850
0.5055 Remote Similarity NPC254540
0.5055 Remote Similarity NPC472607
0.505 Remote Similarity NPC472993
0.5049 Remote Similarity NPC470716
0.5048 Remote Similarity NPC298666
0.5047 Remote Similarity NPC120952

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC293994 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
0.5652 Remote Similarity NPD7054 Phase 4

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