Natural Product: NPC76518

Natural Product IDNPC76518
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IUKHRGYJJZRAQW-XLWCLXEDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL376382
PubChem CID 44423571
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002321] Cycloartanols and derivatives

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 IUKHRGYJJZRAQW-XLWCLXEDSA-N
Standard InCHI InChI=1S/C30H48O2/c1-19(2)22(31)9-8-20(3)21-12-14-28(7)24-11-10-23-26(4,5)25(32)13-15-29(23)18-30(24,29)17-16-27(21,28)6/h20-21,23-25,32H,1,8-18H2,2-7H3/t20-,21-,23+,24+,25+,27-,28+,29-,30+/m1/s1
SMILES CC(=C)C(=O)CC[C@H]([C@H]1CC[C@@]2([C@]1(C)CC[C@@]13[C@H]2CC[C@@H]2[C@]3(C1)CC[C@@H](C2(C)C)O)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
NPO33132 bryonia dioica Species Cucurbitaceae Eukaryota Roots n.a. n.a. PMID[11858752]
NPO33132 bryonia dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[17503850]

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
NPT80 Cell line Raji Homo sapiens Activity = 70.0 % PMID[18494522]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 1.5 % PubChem BioAssay data set
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 25.4 % PMID[20591538]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 73.1 % PMID[15620243]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 97.8 % PMID[11473410]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 IC50 = 9.3 nM PMID[22037378]
NPT2 Others Unspecified n.a. Activity = 1.4 n.a. PMID[7760075]

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 NPC76518 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
0.8 Intermediate Similarity NPC273366
0.7255 Intermediate Similarity NPC331618
0.7255 Intermediate Similarity NPC257191
0.7255 Intermediate Similarity NPC196358
0.7115 Intermediate Similarity NPC200243
0.7115 Intermediate Similarity NPC254509
0.7059 Intermediate Similarity NPC607543
0.6981 Remote Similarity NPC472342
0.6863 Remote Similarity NPC41577
0.6852 Remote Similarity NPC22133
0.6792 Remote Similarity NPC85346
0.6792 Remote Similarity NPC65897
0.6792 Remote Similarity NPC80237
0.6792 Remote Similarity NPC477857
0.6786 Remote Similarity NPC89747
0.6731 Remote Similarity NPC299948
0.6731 Remote Similarity NPC241085
0.6724 Remote Similarity NPC483817
0.6667 Remote Similarity NPC195530
0.6481 Remote Similarity NPC604180
0.6429 Remote Similarity NPC472341
0.6364 Remote Similarity NPC470830
0.6364 Remote Similarity NPC479659
0.6316 Remote Similarity NPC12722
0.6271 Remote Similarity NPC18384
0.6207 Remote Similarity NPC473238
0.6182 Remote Similarity NPC82623
0.6034 Remote Similarity NPC477858
0.6 Remote Similarity NPC110923
0.6 Remote Similarity NPC74296
0.5965 Remote Similarity NPC70982
0.5932 Remote Similarity NPC134481
0.5932 Remote Similarity NPC606508
0.5862 Remote Similarity NPC67872
0.5806 Remote Similarity NPC195366
0.5806 Remote Similarity NPC114743
0.569 Remote Similarity NPC473279
0.5645 Remote Similarity NPC307776
0.5593 Remote Similarity NPC282275
0.5556 Remote Similarity NPC85379
0.5556 Remote Similarity NPC144909
0.5556 Remote Similarity NPC476304
0.5517 Remote Similarity NPC145552
0.5484 Remote Similarity NPC476186
0.5424 Remote Similarity NPC49168
0.5424 Remote Similarity NPC5046
0.5323 Remote Similarity NPC479660
0.5254 Remote Similarity NPC107704
0.5246 Remote Similarity NPC195489
0.5167 Remote Similarity NPC168824
0.5167 Remote Similarity NPC302041
0.5147 Remote Similarity NPC603266
0.5135 Remote Similarity NPC73986
0.5082 Remote Similarity NPC189917
0.5082 Remote Similarity NPC264602
0.5082 Remote Similarity NPC96812
0.5082 Remote Similarity NPC39462

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC76518 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