Natural Product: NPC140969

Natural Product IDNPC140969
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VRHZMFGDDGFRLP-AFHBHXEDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 46173999
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans

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 VRHZMFGDDGFRLP-AFHBHXEDSA-N
Standard InCHI InChI=1S/C20H22O6/c1-23-17-5-3-11(7-15(17)21)19-13-9-26-20(14(13)10-25-19)12-4-6-18(24-2)16(22)8-12/h3-8,13-14,19-22H,9-10H2,1-2H3/t13-,14-,19+,20+/m0/s1
SMILES COc1ccc(cc1O)[C@@H]1[C@H]2CO[C@H](c3ccc(c(c3)O)OC)[C@H]2CO1

  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
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[15387651]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[17841110]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota roots and rhizomes Shaoguan, Guangdong Province, China 2007-Dec PMID[20540535]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20778930]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16314.1 Clematis terniflora var. mandshurica Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9693 Clematis manshurica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10868 Clematis hexapetala Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16314.1 Clematis terniflora var. mandshurica Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10868 Clematis hexapetala Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6583 Clematis chinensis Species Ranunculaceae 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 NPC140969 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
0.6512 Remote Similarity NPC115207
0.6512 Remote Similarity NPC158079
0.6512 Remote Similarity NPC228346
0.6512 Remote Similarity NPC40432
0.6512 Remote Similarity NPC161557
0.6341 Remote Similarity NPC141765
0.6341 Remote Similarity NPC34103
0.625 Remote Similarity NPC27843
0.625 Remote Similarity NPC7171
0.6 Remote Similarity NPC207400
0.5957 Remote Similarity NPC126409
0.5957 Remote Similarity NPC99572
0.5952 Remote Similarity NPC121783
0.5952 Remote Similarity NPC34902
0.5952 Remote Similarity NPC18449
0.5854 Remote Similarity NPC146355
0.5854 Remote Similarity NPC131747
0.5854 Remote Similarity NPC257682
0.566 Remote Similarity NPC88640
0.566 Remote Similarity NPC101153
0.566 Remote Similarity NPC193666
0.566 Remote Similarity NPC123526
0.566 Remote Similarity NPC608725
0.5652 Remote Similarity NPC165155
0.5652 Remote Similarity NPC24490
0.5645 Remote Similarity NPC279298
0.5625 Remote Similarity NPC487684
0.5577 Remote Similarity NPC298317
0.5577 Remote Similarity NPC255566
0.551 Remote Similarity NPC487683
0.551 Remote Similarity NPC479434
0.5435 Remote Similarity NPC222127
0.5435 Remote Similarity NPC82862
0.5319 Remote Similarity NPC606146
0.5238 Remote Similarity NPC281864
0.5238 Remote Similarity NPC328682
0.5238 Remote Similarity NPC54321
0.5102 Remote Similarity NPC227160
0.5102 Remote Similarity NPC82111
0.5094 Remote Similarity NPC135777
0.5094 Remote Similarity NPC223185
0.5094 Remote Similarity NPC610778

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC140969 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