Natural Product: NPC119309

Natural Product IDNPC119309
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 INNVZBQBNNATQV-ASPVKUGASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101023288
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000137] Resorcinols

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 INNVZBQBNNATQV-ASPVKUGASA-N
Standard InCHI InChI=1S/C28H38O4/c29-25-17-23(18-26(30)21-25)15-13-11-9-7-5-3-1-2-4-6-8-10-12-14-16-24-19-27(31)22-28(32)20-24/h1,3-4,6,17-22,29-32H,2,5,7-16H2/b3-1+,6-4+
SMILES C(=CCCCCCCc1cc(cc(c1)O)O)/C/C=C/CCCCCc1cc(cc(c1)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
NPO8945 Grevillea robusta Species Proteaceae Eukaryota leaves n.a. n.a. PMID[17243726]
NPO8945 Grevillea robusta Species Proteaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8945 Grevillea robusta Species Proteaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8945 Grevillea robusta Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8945 Grevillea robusta Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8945 Grevillea robusta Species Proteaceae 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 NPC119309 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
0.9167 High Similarity NPC71002
0.9167 High Similarity NPC10588
0.9167 High Similarity NPC302219
0.9167 High Similarity NPC242342
0.9167 High Similarity NPC249828
0.9167 High Similarity NPC85479
0.9091 High Similarity NPC470700
0.9091 High Similarity NPC54844
0.9091 High Similarity NPC39097
0.9091 High Similarity NPC302681
0.9091 High Similarity NPC118286
0.9091 High Similarity NPC109691
0.8919 High Similarity NPC72947
0.8571 High Similarity NPC53051
0.8571 High Similarity NPC24404
0.8571 High Similarity NPC313030
0.8571 High Similarity NPC39664
0.8333 Intermediate Similarity NPC146798
0.8333 Intermediate Similarity NPC222522
0.8333 Intermediate Similarity NPC106396
0.8333 Intermediate Similarity NPC94351
0.8333 Intermediate Similarity NPC168303
0.7895 Intermediate Similarity NPC166761
0.7273 Intermediate Similarity NPC246056
0.725 Intermediate Similarity NPC284011
0.6744 Remote Similarity NPC210497
0.6744 Remote Similarity NPC192
0.6667 Remote Similarity NPC294186
0.6667 Remote Similarity NPC158253
0.6667 Remote Similarity NPC147310
0.6667 Remote Similarity NPC137415
0.6667 Remote Similarity NPC204901
0.6667 Remote Similarity NPC166313
0.6667 Remote Similarity NPC192032
0.6667 Remote Similarity NPC24407
0.6667 Remote Similarity NPC11280
0.6522 Remote Similarity NPC305603
0.6522 Remote Similarity NPC61033
0.6522 Remote Similarity NPC127894
0.6522 Remote Similarity NPC470759
0.6327 Remote Similarity NPC140521
0.619 Remote Similarity NPC483454
0.619 Remote Similarity NPC162314
0.6154 Remote Similarity NPC241891
0.6154 Remote Similarity NPC134829
0.6087 Remote Similarity NPC470760
0.6047 Remote Similarity NPC94139
0.6047 Remote Similarity NPC147284
0.5952 Remote Similarity NPC232523
0.5814 Remote Similarity NPC488413
0.5814 Remote Similarity NPC488412
0.5686 Remote Similarity NPC123559
0.5652 Remote Similarity NPC48730
0.5652 Remote Similarity NPC219070
0.5581 Remote Similarity NPC486908
0.551 Remote Similarity NPC249836
0.5306 Remote Similarity NPC248396
0.5294 Remote Similarity NPC470699
0.5227 Remote Similarity NPC487734
0.5217 Remote Similarity NPC114064
0.5208 Remote Similarity NPC483450
0.52 Remote Similarity NPC15860
0.5192 Remote Similarity NPC473221
0.5111 Remote Similarity NPC487735
0.5102 Remote Similarity NPC112596

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC119309 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