Natural Product: NPC82902

Natural Product IDNPC82902
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Kulinone
IUPAC Name (5R,9R,10R,13S,14S,16S,17S)-16-hydroxy-4,4,10,13,14-pentamethyl-17-[(2R)-6-methylhept-5-en-2-yl]-1,2,5,6,9,11,12,15,16,17-decahydrocyclopenta[a]phenanthren-3-one
Synonyms Kulinone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL464491
PubChem CID 44567124
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 YORJEFOAAXJWIS-QOXWJFHWSA-N
Standard InCHI InChI=1S/C30H48O2/c1-19(2)10-9-11-20(3)26-23(31)18-30(8)22-12-13-24-27(4,5)25(32)15-16-28(24,6)21(22)14-17-29(26,30)7/h10,12,20-21,23-24,26,31H,9,11,13-18H2,1-8H3/t20-,21+,23+,24+,26-,28-,29+,30-/m1/s1
SMILES CC(=CCC[C@@H](C)[C@@H]1[C@H](C[C@]2(C)C3=CC[C@H]4C(C)(C)C(=O)CC[C@]4(C)[C@H]3CC[C@@]12C)O)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
NPO18596 Melia dubia Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[12502333]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. Brazilian n.a. PMID[15387656]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. ripe fruit n.a. PMID[16205005]
NPO31089 Melia toosendan Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[19341288]
NPO31089 Melia toosendan Species Meliaceae Eukaryota n.a. fruit n.a. PMID[20961091]
NPO31089 Melia toosendan Species Meliaceae Eukaryota fruits Wanyuan County, Sichuan Province, China 2007-OCT PMID[20961091]
NPO18932 Melia azedarach Species Meliaceae Eukaryota Fruits n.a. n.a. PMID[33253570]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[36362399]
NPO18932 Melia azedarach Species Meliaceae Eukaryota Seeds n.a. n.a. PMID[3701342]
NPO18596 Melia dubia Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31089 Melia toosendan Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31089 Melia toosendan Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18596 Melia dubia Species Meliaceae 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
NPT168 Cell line P388 Mus musculus ED50 = 4.6 ug ml-1 PMID[12502333]
NPT83 Cell line MCF7 Homo sapiens GI50 = 3.6 ug.mL-1 PMID[12502333]
NPT395 Cell line SF-268 Homo sapiens GI50 = 3.6 ug.mL-1 PMID[12502333]
NPT575 Cell line KM-20L2 Homo sapiens GI50 = 3.6 ug.mL-1 PMID[12502333]
NPT397 Cell line NCI-H460 Homo sapiens GI50 = 3.6 ug.mL-1 PMID[12502333]
NPT1081 Cell line BXPC-3 Homo sapiens GI50 = 3.61 ug.mL-1 PMID[12502333]
NPT90 Cell line DU-145 Homo sapiens GI50 = 3.6 ug.mL-1 PMID[12502333]
NPT168 Cell line P388 Mus musculus ED50 = 1.7 ug ml-1 PMID[20961091]
NPT1045 Cell line U2OS Homo sapiens IC50 = 6.9 ug.mL-1 PMID[20961091]
NPT83 Cell line MCF7 Homo sapiens IC50 = 42.5 ug.mL-1 PMID[20961091]

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 NPC82902 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
0.8571 High Similarity NPC474218
0.7966 Intermediate Similarity NPC2983
0.7966 Intermediate Similarity NPC469994
0.7742 Intermediate Similarity NPC154101
0.7581 Intermediate Similarity NPC317590
0.7302 Intermediate Similarity NPC320026
0.7097 Intermediate Similarity NPC171441
0.6833 Remote Similarity NPC1319
0.6818 Remote Similarity NPC107243
0.6471 Remote Similarity NPC218383
0.6471 Remote Similarity NPC474327
0.6286 Remote Similarity NPC57416
0.5909 Remote Similarity NPC90652
0.5909 Remote Similarity NPC155255
0.5909 Remote Similarity NPC260992
0.5672 Remote Similarity NPC470417
0.5652 Remote Similarity NPC471224
0.5652 Remote Similarity NPC486521
0.5652 Remote Similarity NPC262870
0.5652 Remote Similarity NPC28227
0.5571 Remote Similarity NPC67831
0.5571 Remote Similarity NPC174051
0.5538 Remote Similarity NPC470078
0.5507 Remote Similarity NPC147066
0.5441 Remote Similarity NPC470052
0.5395 Remote Similarity NPC484792
0.5373 Remote Similarity NPC470223
0.5362 Remote Similarity NPC470047
0.5362 Remote Similarity NPC470046
0.5352 Remote Similarity NPC472239
0.5342 Remote Similarity NPC273669
0.5342 Remote Similarity NPC484802
0.5342 Remote Similarity NPC118647
0.5278 Remote Similarity NPC479667
0.5278 Remote Similarity NPC605437
0.527 Remote Similarity NPC73506
0.5224 Remote Similarity NPC247220
0.52 Remote Similarity NPC140723
0.5195 Remote Similarity NPC189282
0.5195 Remote Similarity NPC237402
0.5139 Remote Similarity NPC484798
0.5132 Remote Similarity NPC63023
0.5132 Remote Similarity NPC121566
0.5132 Remote Similarity NPC100955
0.5132 Remote Similarity NPC95243
0.5072 Remote Similarity NPC133954
0.507 Remote Similarity NPC318390

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC82902 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