Natural Product: NPC575491

Natural Product IDNPC575491
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (7~{R},9~{R})-9-acetyl-7-[(2~{R},4~{R},5~{R},6~{R})-4-amino-5-[(1~{R},3~{R})-3-hydroxy-1-[(1~{S})-2-hydroxy-1-methyl-ethoxy]butoxy]-6-methyl-tetrahydropyran-2-yl]oxy-4,6,9,11-tetrahydroxy-8,10-dihydro-7~{H}-tetracene-5,12-dione
IUPAC Name (7~{R},9~{R})-9-acetyl-7-[(2~{R},4~{R},5~{R},6~{R})-4-amino-5-[(1~{R},3~{R})-3-hydroxy-1-[(1~{S})-2-hydroxy-1-methyl-ethoxy]butoxy]-6-methyl-tetrahydropyran-2-yl]oxy-4,6,9,11-tetrahydroxy-8,10-dihydro-7~{H}-tetracene-5,12-dione
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002106] Anthracyclines

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 DNHXZQIEIKSDIK-MBNSOBSASA-N
Standard InCHI InChI=1S/C33H41NO13/c1-13(36)8-22(44-14(2)12-35)47-32-15(3)45-23(9-19(32)34)46-21-11-33(43,16(4)37)10-18-25(21)31(42)27-26(29(18)40)28(39)17-6-5-7-20(38)24(17)30(27)41/h5-7,13-15,19,21-23,32,35-36,38,40,42-43H,8-12,34H2,1-4H3/t13-,14+,15-,19-,21-,22-,23+,32+,33-/m1/s1
SMILES CC(=O)[C@@]1(O)CC2=C(O)C3=C(C(=O)C4=C(O)C=CC=C4C3=O)C(O)=C2[C@H](O[C@H]2C[C@@H](N)[C@@H](O[C@H](C[C@@H](C)O)O[C@@H](C)CO)[C@@H](C)O2)C1

  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
NPO48928 Actinomadura roseoviolacea var. biwakoensis nov. var. Genus Thermomonosporaceae Bacteria n.a. n.a. n.a. Database[COCONUT]

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

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 NPC575491 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
0.6118 Remote Similarity NPC611971
0.6023 Remote Similarity NPC602774
0.5638 Remote Similarity NPC487390
0.5532 Remote Similarity NPC109403
0.5474 Remote Similarity NPC487573
0.5253 Remote Similarity NPC487386
0.5204 Remote Similarity NPC261012
0.5204 Remote Similarity NPC314738
0.5152 Remote Similarity NPC468994

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC575491 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
0.6118 Remote Similarity NPD6535 Phase 4
0.6047 Remote Similarity NPD6534 Approved
0.5686 Remote Similarity NPD7696 Phase 3
0.5686 Remote Similarity NPD7697 Phase 3
0.5686 Remote Similarity NPD7698 Approved
0.5532 Remote Similarity NPD6778 Phase 4
0.5474 Remote Similarity NPD6777 Approved
0.5464 Remote Similarity NPD7699 Phase 2
0.5464 Remote Similarity NPD7700 Phase 2
0.5437 Remote Similarity NPD7871 Phase 2
0.5385 Remote Similarity NPD7870 Phase 2
0.5204 Remote Similarity NPD6781 Phase 4
0.5204 Remote Similarity NPD6782 Phase 4
0.5158 Remote Similarity NPD7211 Clinical (unspecified phase)
0.5152 Remote Similarity NPD6779 Approved
0.5152 Remote Similarity NPD6780 Approved

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