Natural Product: NPC62107

Natural Product IDNPC62107
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FYSSBMZUBSBFJL-SECBINFHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5312798
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000299] Medium-chain hydroxy acids 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 FYSSBMZUBSBFJL-SECBINFHSA-N
Standard InCHI InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1
SMILES CCCCCCC[C@H](CC(=O)O)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
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota Aerial parts n.a. n.a. PMID[20166702]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. aerial part n.a. PMID[21171571]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. PMID[29094598]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11266 Garcinia cambogia Species Clusiaceae 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

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 NPC62107 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
1.0 High Similarity NPC200618
1.0 High Similarity NPC131770
1.0 High Similarity NPC90904
0.625 Remote Similarity NPC324004
0.625 Remote Similarity NPC328497
0.52 Remote Similarity NPC250870
0.52 Remote Similarity NPC490959
0.52 Remote Similarity NPC191084
0.5172 Remote Similarity NPC171736
0.5172 Remote Similarity NPC301585
0.5172 Remote Similarity NPC261080
0.5172 Remote Similarity NPC132565
0.5172 Remote Similarity NPC209970
0.5172 Remote Similarity NPC216630
0.5172 Remote Similarity NPC201844
0.5172 Remote Similarity NPC301696
0.5172 Remote Similarity NPC196924
0.5172 Remote Similarity NPC307783
0.5172 Remote Similarity NPC154186
0.5172 Remote Similarity NPC149184
0.5172 Remote Similarity NPC279026
0.5172 Remote Similarity NPC113928
0.5172 Remote Similarity NPC14227

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC62107 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
0.5172 Remote Similarity NPD2270 Pre-clinical
0.5172 Remote Similarity NPD633 Phase 3
0.5172 Remote Similarity NPD9448 Phase 2

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