Natural Product: NPC137780

Natural Product IDNPC137780
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XFZJEEAOWLFHDH-DQPHOHOGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 442677
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 XFZJEEAOWLFHDH-DQPHOHOGSA-N
Standard InCHI InChI=1S/C30H26O12/c31-13-7-20(37)24-23(8-13)41-29(12-2-4-16(33)19(36)6-12)27(40)26(24)25-21(38)10-17(34)14-9-22(39)28(42-30(14)25)11-1-3-15(32)18(35)5-11/h1-8,10,22,26-29,31-40H,9H2/t22-,26+,27+,28-,29+/m0/s1
SMILES c1cc(c(cc1[C@H]1[C@H](Cc2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4ccc(c(c4)O)O)[C@@H]3O)O)O)c2O1)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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11240-015-0761-z]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s12010-013-0354-4]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1055/S-2006-958077]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1186/s40064-015-0831-z]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1501/Tarimbil_0000001065]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[37446586]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO8561 Liparis loeselii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16080 Cedrela fissilis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8561 Liparis loeselii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9505 Magnolia pterocarpa Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO870 Aglaia tsangii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8561 Liparis loeselii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16781 Dorycnium suffruticosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17525 Baccharis sagittalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26159 Pseudocyphellaria faveolata Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17773 Senecio ambraceus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4024 Pedicularis procera Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27966 Stigmatella erecta Species Archangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6863 Dendrobates azureus Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17165 Teucrium heterophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16080 Cedrela fissilis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13761 Plexaurella nutans Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14281 Anaxagorea dolichocarpa Species Annonaceae 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 NPC137780 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
1.0 High Similarity NPC58190
1.0 High Similarity NPC108811
1.0 High Similarity NPC170103
1.0 High Similarity NPC236202
1.0 High Similarity NPC262911
1.0 High Similarity NPC202742
0.9821 High Similarity NPC246202
0.9821 High Similarity NPC224161
0.9821 High Similarity NPC46335
0.9821 High Similarity NPC279406
0.9821 High Similarity NPC486519
0.873 High Similarity NPC278548
0.8305 Intermediate Similarity NPC96576
0.8226 Intermediate Similarity NPC313116
0.8226 Intermediate Similarity NPC603340
0.8125 Intermediate Similarity NPC226809
0.7969 Intermediate Similarity NPC70409
0.7969 Intermediate Similarity NPC204770
0.7969 Intermediate Similarity NPC600551
0.7969 Intermediate Similarity NPC601980
0.7969 Intermediate Similarity NPC602065
0.7969 Intermediate Similarity NPC611024
0.7727 Intermediate Similarity NPC600630
0.7727 Intermediate Similarity NPC607896
0.7727 Intermediate Similarity NPC611369
0.7639 Intermediate Similarity NPC86630
0.7619 Intermediate Similarity NPC294558
0.7619 Intermediate Similarity NPC18185
0.7619 Intermediate Similarity NPC263940
0.7606 Intermediate Similarity NPC147743
0.7606 Intermediate Similarity NPC4809
0.7606 Intermediate Similarity NPC73517
0.7576 Intermediate Similarity NPC211561
0.7534 Intermediate Similarity NPC106601
0.7534 Intermediate Similarity NPC151474
0.7432 Intermediate Similarity NPC212614
0.7432 Intermediate Similarity NPC205613
0.7288 Intermediate Similarity NPC178054
0.7188 Intermediate Similarity NPC601999
0.7143 Intermediate Similarity NPC159526
0.7059 Intermediate Similarity NPC601997
0.7059 Intermediate Similarity NPC609211
0.7059 Intermediate Similarity NPC610665
0.7018 Intermediate Similarity NPC261619
0.7018 Intermediate Similarity NPC61477
0.7018 Intermediate Similarity NPC78770
0.7018 Intermediate Similarity NPC219876
0.7018 Intermediate Similarity NPC126029
0.7018 Intermediate Similarity NPC15658
0.6857 Remote Similarity NPC302549
0.6716 Remote Similarity NPC184245
0.6716 Remote Similarity NPC187801
0.6716 Remote Similarity NPC610920
0.6667 Remote Similarity NPC20050
0.6623 Remote Similarity NPC78074
0.6575 Remote Similarity NPC306267
0.6486 Remote Similarity NPC135021
0.6479 Remote Similarity NPC272552
0.6479 Remote Similarity NPC226108
0.6479 Remote Similarity NPC322899
0.6447 Remote Similarity NPC9309
0.641 Remote Similarity NPC478340
0.6389 Remote Similarity NPC46283
0.6389 Remote Similarity NPC469944
0.6351 Remote Similarity NPC478616
0.6351 Remote Similarity NPC478339
0.6329 Remote Similarity NPC478337
0.6329 Remote Similarity NPC478338
0.6301 Remote Similarity NPC44192
0.6176 Remote Similarity NPC277331
0.6176 Remote Similarity NPC100482
0.6145 Remote Similarity NPC478617
0.5946 Remote Similarity NPC65333
0.5946 Remote Similarity NPC134911
0.5942 Remote Similarity NPC82917
0.5833 Remote Similarity NPC207179
0.5833 Remote Similarity NPC167571
0.5833 Remote Similarity NPC278552
0.5775 Remote Similarity NPC165483
0.5769 Remote Similarity NPC471404
0.5732 Remote Similarity NPC479793
0.5694 Remote Similarity NPC28440
0.5616 Remote Similarity NPC155564
0.5595 Remote Similarity NPC479794
0.5574 Remote Similarity NPC268266
0.5574 Remote Similarity NPC42760
0.5574 Remote Similarity NPC220825
0.5574 Remote Similarity NPC268342
0.5455 Remote Similarity NPC171932
0.5417 Remote Similarity NPC20757
0.5417 Remote Similarity NPC227516
0.541 Remote Similarity NPC601844
0.5224 Remote Similarity NPC16435
0.5169 Remote Similarity NPC185231
0.5152 Remote Similarity NPC36835
0.5152 Remote Similarity NPC246162
0.5152 Remote Similarity NPC9743
0.5152 Remote Similarity NPC260491
0.5152 Remote Similarity NPC61506
0.5152 Remote Similarity NPC240476
0.5072 Remote Similarity NPC150670

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC137780 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
0.7018 Intermediate Similarity NPD1612 Clinical (unspecified phase)
0.7018 Intermediate Similarity NPD1613 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