Natural Product: NPC607515

Natural Product IDNPC607515
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BAYHEZUZRPMUDM-RZHPVIQDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL309787
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 BAYHEZUZRPMUDM-RZHPVIQDSA-N
Standard InCHI InChI=1S/C35H42O9/c1-19-26(39)18-25-31(41-21(3)36)30-20(2)27(44-28(40)15-14-24-12-10-9-11-13-24)16-17-35(30,8)33(43-23(5)38)32(42-22(4)37)29(19)34(25,6)7/h9-15,25,27,30-33H,2,16-18H2,1,3-8H3/b15-14+/t25-,27-,30-,31+,32+,33-,35+/m0/s1
SMILES C=C1[C@@H](OC(=O)/C=C/c2ccccc2)CC[C@@]2(C)[C@@H](OC(C)=O)[C@H](OC(C)=O)C3=C(C)C(=O)C[C@@H]([C@@H](OC(C)=O)[C@H]12)C3(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
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.plantsci.2006.08.002]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(00)00306-X]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(01)00432-0]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np990201k]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota Needles n.a. n.a. PMID[11325226]
NPO27746 Taxus mairei Species Taxaceae Eukaryota stem bark n.a. n.a. PMID[11473432]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12217376]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. Japan n.a. PMID[14987066]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[15844936]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. Japan n.a. PMID[15974623]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[15974623]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[23265441]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[7561894]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[7908950]
NPO27746 Taxus mairei Species Taxaceae Eukaryota Roots n.a. n.a. PMID[8991951]
NPO41064 Taxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9461653]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9644081]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO60137 Taxus baccata L. Genus Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO41064 Taxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31343 Taxus chinensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5067 Taxus baccata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13290 Taxus canadensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27746 Taxus mairei Species Taxaceae 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
NPT137 Cell line L1210 Mus musculus IC50 > 10.0 ug.mL-1 DOI[10.1016/S0960-894X(97)00029-2]
NPT168 Cell line P388 Mus musculus IC50 = 10000000.0 nM DOI[10.1016/S0960-894X(97)00439-3]
NPT28438 Unchecked Unchecked n.a. Control = 571.0 % DOI[10.1016/S0960-894X(97)00029-2]
NPT28438 Unchecked Unchecked n.a. Relative activity = 77.0 n.a. PMID[10617080]
NPT28438 Unchecked Unchecked n.a. Control = 195.0 % DOI[10.1016/S0960-894X(97)00029-2]
NPT28438 Unchecked Unchecked n.a. Control = 571.0 % PMID[10091690]
NPT28438 Unchecked Unchecked n.a. Control = 195.0 % PMID[10091690]

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 NPC607515 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
0.9403 High Similarity NPC472361
0.8971 High Similarity NPC472437
0.8194 Intermediate Similarity NPC475493
0.8028 Intermediate Similarity NPC473749
0.8026 Intermediate Similarity NPC472371
0.7917 Intermediate Similarity NPC195224
0.7432 Intermediate Similarity NPC469742
0.7297 Intermediate Similarity NPC472394
0.7273 Intermediate Similarity NPC472388
0.7273 Intermediate Similarity NPC608702
0.725 Intermediate Similarity NPC475400
0.7143 Intermediate Similarity NPC472418
0.7051 Intermediate Similarity NPC473541
0.7013 Intermediate Similarity NPC225103
0.6923 Remote Similarity NPC473443
0.6923 Remote Similarity NPC209851
0.6835 Remote Similarity NPC471880
0.6761 Remote Similarity NPC472389
0.6456 Remote Similarity NPC473423
0.641 Remote Similarity NPC472395
0.6329 Remote Similarity NPC473439
0.622 Remote Similarity NPC472373
0.622 Remote Similarity NPC184109
0.6 Remote Similarity NPC89324
0.5783 Remote Similarity NPC12016
0.561 Remote Similarity NPC472374
0.5556 Remote Similarity NPC605842
0.5263 Remote Similarity NPC8196
0.5176 Remote Similarity NPC300827
0.5057 Remote Similarity NPC471758

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607515 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