Natural Product: NPC42384

Natural Product IDNPC42384
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Guttiferone K
IUPAC Name n.a.
Synonyms Guttiferone K
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL388529
PubChem CID NA
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001564] Bicyclic monoterpenoids

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 QKKRBNPMUBNTPA-ZZEFGTIFSA-N
Standard InCHI InChI=1S/C38H50O6/c1-23(2)11-10-18-36(9)28(14-12-24(3)4)22-37(19-16-25(5)6)33(42)31(32(41)27-13-15-29(39)30(40)21-27)34(43)38(36,35(37)44)20-17-26(7)8/h11-13,15-17,21,28,39-40,42H,10,14,18-20,22H2,1-9H3/t28-,36+,37+,38-/m1/s1
SMILES CC(=CC[C@]12C[C@@H](CC=C(C)C)[C@]([C@@](C2=O)(C(=O)C(=C1O)C(=O)c1ccc(c(c1)O)O)CC=C(C)C)(C)CCC=C(C)C)C

  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
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1071/CH03175]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17287127]
NPO17459 Rheedia calcicola Species Clusiaceae Eukaryota n.a. Madagascar rain forest n.a. PMID[17348706]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[20058933]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota young fruits Khokkhon, Tha Bo District, Nong Khai Province, Thailand 2011-Aug PMID[25651042]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota flowers Pakook, Muang District, Chiang Rai Province, Thailand 2013-Feb PMID[25651042]
NPO40144 Garcinia schomburgkiana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[27409517]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota Leaves n.a. n.a. PMID[31860303]
NPO40144 Garcinia schomburgkiana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1330 Stachybotrys alternans Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2382 Nicotiana excelsior Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12849 Lagerstroemia subcostata Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17459 Rheedia calcicola Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24463 Linum corymbulosum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO769 Eria elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2382 Nicotiana excelsior Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1330 Stachybotrys alternans Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6536 Marrubium velutinum Species Lamiaceae 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
NPT1044 Individual protein DNA topoisomerase II alpha Homo sapiens Vmax(app) = 110.8 mM/min PMID[31618025]
NPT1044 Individual protein DNA topoisomerase II alpha Homo sapiens Vmax(app) = 93.0 mM/min PMID[31618025]
NPT1044 Individual protein DNA topoisomerase II alpha Homo sapiens Vmax(app) = 114.6 mM/min PMID[31618025]
NPT3732 Individual protein DNA polymerase lambda Homo sapiens IC50 = 5400.0 nM PMID[27409517]
NPT37 Individual protein Signal transducer and activator of transcription 1-alpha/beta Homo sapiens Kd = 20600.0 nM PMID[24417609]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT179 Cell line A2780 Homo sapiens IC50 = 3.6 ug.mL-1 PMID[17348706]
NPT139 Cell line HT-29 Homo sapiens IC50 = 5400.0 nM PMID[20058933]

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 NPC42384 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 NPC289358
1.0 High Similarity NPC4289
0.9091 High Similarity NPC5014
0.8939 High Similarity NPC23667
0.8939 High Similarity NPC157284
0.8485 Intermediate Similarity NPC198803
0.8382 Intermediate Similarity NPC482621
0.831 Intermediate Similarity NPC482618
0.8194 Intermediate Similarity NPC482617
0.8194 Intermediate Similarity NPC482616
0.8125 Intermediate Similarity NPC149773
0.7714 Intermediate Similarity NPC165191
0.7714 Intermediate Similarity NPC177501
0.7681 Intermediate Similarity NPC48949
0.7639 Intermediate Similarity NPC25736
0.7571 Intermediate Similarity NPC114333
0.7571 Intermediate Similarity NPC28592
0.7571 Intermediate Similarity NPC51531
0.7465 Intermediate Similarity NPC473479
0.7465 Intermediate Similarity NPC50615
0.7465 Intermediate Similarity NPC141650
0.7222 Intermediate Similarity NPC30846
0.7042 Intermediate Similarity NPC46242
0.7042 Intermediate Similarity NPC91887
0.7042 Intermediate Similarity NPC93556
0.6944 Remote Similarity NPC297797
0.6757 Remote Similarity NPC469857
0.6757 Remote Similarity NPC245760
0.6579 Remote Similarity NPC471971
0.6579 Remote Similarity NPC471972
0.6579 Remote Similarity NPC469855
0.6447 Remote Similarity NPC294330
0.6282 Remote Similarity NPC469856
0.6232 Remote Similarity NPC259400
0.6232 Remote Similarity NPC130591
0.6232 Remote Similarity NPC234637
0.6203 Remote Similarity NPC471970
0.6154 Remote Similarity NPC469854
0.6154 Remote Similarity NPC482619
0.6104 Remote Similarity NPC479148
0.6027 Remote Similarity NPC473779
0.6026 Remote Similarity NPC479151
0.5833 Remote Similarity NPC482620
0.575 Remote Similarity NPC603871
0.5679 Remote Similarity NPC237441
0.5616 Remote Similarity NPC611064
0.5443 Remote Similarity NPC473527
0.5422 Remote Similarity NPC479146

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC42384 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