Natural Product: NPC38893

Natural Product IDNPC38893
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (4Bs,8As,9R)-4B,8,8-Trimethyl-2-Propan-2-Yl-5,6,7,8A,9,10-Hexahydrophenanthrene-3,9-Diol
IUPAC Name (4bS,8aS,9R)-4b,8,8-trimethyl-2-propan-2-yl-5,6,7,8a,9,10-hexahydrophenanthrene-3,9-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1094422
PubChem CID 14378752
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

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 XEJHUBFVQWSNJW-WSTZPKSXSA-N
Standard InCHI InChI=1S/C20H30O2/c1-12(2)14-9-13-10-17(22)18-19(3,4)7-6-8-20(18,5)15(13)11-16(14)21/h9,11-12,17-18,21-22H,6-8,10H2,1-5H3/t17-,18+,20-/m1/s1
SMILES CC(C)c1cc2C[C@H]([C@H]3C(C)(C)CCC[C@]3(C)c2cc1O)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
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19481938]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28294615]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31291099]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11576 Glycosmis macrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22691 Mentha cardiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6289 Ceropegia dichotoma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23384 Rhodiola semenovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10638 Plectranthus myrianthus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3873 Crotalaria candicans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11843 Stephania zippeliana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12565 Hypericum polyanthemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11190 Veronica polita Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5043 Eria japonica Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8934 Gypsophila perfoliata Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9532 Vernonia cistifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10605 Tristania conferta Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5456 Juniperus drupacea Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21720 Talaromyces variabilis Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7822.1 Eucalyptus globulus subsp. bicostata Subspecies Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12091 Martensia denticulata Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO526 Salvia sessei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1815 Breonia chinensis Species Rubiaceae 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
NPT1605 Organism Enterococcus Enterococcus MIC = 4.0 ug.mL-1 PMID[25440884]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 4.0 ug.mL-1 PMID[25440884]

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 NPC38893 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
0.6667 Remote Similarity NPC469644
0.6538 Remote Similarity NPC92
0.6538 Remote Similarity NPC260323
0.6316 Remote Similarity NPC471077
0.625 Remote Similarity NPC78307
0.6071 Remote Similarity NPC604431
0.6034 Remote Similarity NPC227719
0.5893 Remote Similarity NPC192948
0.5893 Remote Similarity NPC35797
0.5714 Remote Similarity NPC471671
0.5636 Remote Similarity NPC176279
0.5614 Remote Similarity NPC11250
0.5614 Remote Similarity NPC172219
0.5614 Remote Similarity NPC304510
0.5345 Remote Similarity NPC181334
0.5254 Remote Similarity NPC137750
0.5246 Remote Similarity NPC58560
0.5172 Remote Similarity NPC3009
0.5172 Remote Similarity NPC250323
0.5172 Remote Similarity NPC469663
0.5172 Remote Similarity NPC308311
0.5172 Remote Similarity NPC150601
0.5167 Remote Similarity NPC479465
0.5085 Remote Similarity NPC176130
0.5085 Remote Similarity NPC606176
0.5085 Remote Similarity NPC606869

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC38893 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