Natural Product: NPC76648

Natural Product IDNPC76648
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
PFVZUXQCELCLBL-LVKFHIPRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6852214
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003531] Flavonoid-3-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 PFVZUXQCELCLBL-LVKFHIPRSA-N
Standard InCHI InChI=1S/C27H32O10/c1-12(2)5-10-16-17(28)11-18(29)19-21(31)26(37-27-23(33)22(32)20(30)13(3)35-27)24(36-25(16)19)14-6-8-15(34-4)9-7-14/h6-9,11-13,20,22-23,27-30,32-33H,5,10H2,1-4H3/t13-,20-,22+,23+,27-/m0/s1
SMILES CC(C)CCc1c(cc(c2c(=O)c(c(c3ccc(cc3)OC)oc12)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)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
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[12081149]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. root n.a. PMID[22051934]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. leaf n.a. PMID[24066589]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota aerial parts herbal garden of Chungbuk National University, Cheongju, Korea 2012-Oct PMID[24963714]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. leaf n.a. PMID[8699184]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. aerial part n.a. Database[Article]
NPO19403 Epimedium grandiflorum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13384 Epimedium sempervirens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19403 Epimedium grandiflorum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19403 Epimedium grandiflorum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19403 Epimedium grandiflorum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13384 Epimedium sempervirens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10969 Epimedium sagittatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19403 Epimedium grandiflorum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13384 Epimedium sempervirens Species Berberidaceae 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 NPC76648 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
0.8148 Intermediate Similarity NPC278419
0.8148 Intermediate Similarity NPC179198
0.686 Remote Similarity NPC66087
0.6316 Remote Similarity NPC5319
0.5955 Remote Similarity NPC219904
0.5843 Remote Similarity NPC472459
0.5778 Remote Similarity NPC611303
0.5747 Remote Similarity NPC111929
0.5747 Remote Similarity NPC320283
0.5747 Remote Similarity NPC41121
0.573 Remote Similarity NPC46420
0.5618 Remote Similarity NPC265530
0.5556 Remote Similarity NPC271692
0.5506 Remote Similarity NPC127546
0.5506 Remote Similarity NPC249281
0.5506 Remote Similarity NPC57625
0.5506 Remote Similarity NPC173637
0.5506 Remote Similarity NPC317489
0.5506 Remote Similarity NPC223424
0.5506 Remote Similarity NPC600591
0.5495 Remote Similarity NPC59534
0.5484 Remote Similarity NPC223747
0.5444 Remote Similarity NPC64305
0.5444 Remote Similarity NPC158674
0.5393 Remote Similarity NPC135599
0.5393 Remote Similarity NPC73855
0.5393 Remote Similarity NPC113968
0.5393 Remote Similarity NPC328940
0.5393 Remote Similarity NPC277174
0.5393 Remote Similarity NPC606877
0.5385 Remote Similarity NPC349108
0.5217 Remote Similarity NPC305811
0.5217 Remote Similarity NPC27640
0.5208 Remote Similarity NPC265115
0.5165 Remote Similarity NPC289667
0.5158 Remote Similarity NPC116458
0.5158 Remote Similarity NPC246943
0.5155 Remote Similarity NPC251417
0.5104 Remote Similarity NPC276377
0.5104 Remote Similarity NPC355481
0.5098 Remote Similarity NPC473327
0.5098 Remote Similarity NPC606657
0.5088 Remote Similarity NPC480443
0.5053 Remote Similarity NPC148710
0.5053 Remote Similarity NPC120099

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC76648 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
0.6316 Remote Similarity NPD7804 Clinical (unspecified phase)

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