Natural Product: NPC61013

Natural Product IDNPC61013
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Vincadifformine
IUPAC Name n.a.
Synonyms Vincadifformine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL251690
PubChem CID 94255
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002755] Aspidospermatan-type alkaloids

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 GIGFIWJRTMBSRP-ACRUOGEOSA-N
Standard InCHI InChI=1S/C21H26N2O2/c1-3-20-9-6-11-23-12-10-21(19(20)23)15-7-4-5-8-16(15)22-17(21)14(13-20)18(24)25-2/h4-5,7-8,19,22H,3,6,9-13H2,1-2H3/t19-,20-,21-/m0/s1
SMILES CC[C@]12CCCN3CC[C@@]4(c5ccccc5NC4=C(C1)C(=O)OC)[C@H]23

  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
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[19388660]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[21043460]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. stem n.a. PMID[21043460]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[21043460]
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[21524573]
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28362501]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15819 Hunteria zeylanica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15819 Hunteria zeylanica Species Apocynaceae 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
NPT91 Cell line KB Homo sapiens IC50 = 10.2 ug.mL-1 PMID[17665953]
NPT15 Cell line Jurkat Homo sapiens IC50 = 21.8 ug.mL-1 PMID[17665953]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 6.3 ug.mL-1 PMID[17665953]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 13300.0 nM PMID[17665953]

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 NPC61013 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
0.7639 Intermediate Similarity NPC128948
0.7027 Intermediate Similarity NPC123241
0.6842 Remote Similarity NPC159963
0.6795 Remote Similarity NPC269449
0.6582 Remote Similarity NPC186669
0.625 Remote Similarity NPC293458
0.6173 Remote Similarity NPC14994
0.6098 Remote Similarity NPC485981
0.5833 Remote Similarity NPC97584
0.5513 Remote Similarity NPC25401
0.5513 Remote Similarity NPC248117
0.5513 Remote Similarity NPC238013
0.5422 Remote Similarity NPC22476
0.5375 Remote Similarity NPC224970
0.5375 Remote Similarity NPC193410
0.5375 Remote Similarity NPC167724
0.5375 Remote Similarity NPC223595
0.5357 Remote Similarity NPC203628
0.5309 Remote Similarity NPC203202
0.5309 Remote Similarity NPC264482
0.5294 Remote Similarity NPC5630
0.5244 Remote Similarity NPC99043
0.5244 Remote Similarity NPC218594
0.5119 Remote Similarity NPC475147
0.5116 Remote Similarity NPC303214
0.5114 Remote Similarity NPC189661
0.5057 Remote Similarity NPC6974
0.5057 Remote Similarity NPC87714

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC61013 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