Natural Product: NPC329209

Natural Product IDNPC329209
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VYRAJOITMBSQSE-MTQUCLQASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101921807
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002203] Glycosylamines

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 VYRAJOITMBSQSE-MTQUCLQASA-N
Standard InCHI InChI=1S/C16H23N5O6/c1-8(4-22)2-3-17-14-10-15(19-6-18-14)21(7-20-10)16-13(26)12(25)11(24)9(5-23)27-16/h2,6-7,9,11-13,16,22-26H,3-5H2,1H3,(H,17,18,19)/b8-2-/t9-,11-,12+,13-,16-/m1/s1
SMILES CC(=CCNC1=C2C(=NC=N1)N(C=N2)C3C(C(C(C(O3)CO)O)O)O)CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   381.16 Volume:   354.166
?
Van der Waals volume.
Dense:   1.076 LogP:   -0.527
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.199
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.005
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   17.0
TPSA:   166.01
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   6.0 Rings:   3.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.313 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.104 Fsp3:   0.562
MCE-18:   64.6
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.052 Fluc inhibitor:   0.005
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.04
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.136
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.031 Promiscuous compounds:   0.001

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.724 MDCK Permeability:   -5.296
Pgp-inhibitor:   0.0 Pgp-substrate:   0.873
PAMPA:   1.0
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.984
20% Bioavailability (F20%):   0.594 30% Bioavailability (F30%):   0.99
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.037 MRP1:   0.645
Plasma Protein Binding (PPB):   49.339% Volume Distribution (VD):   -0.269
Fu: 49.715%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.003
OATP1B3 inhibitor:   0.39 BCRP inhibitor:   0.151
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.119 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.892
HLM stability:   0.0
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  7.045 Half-life (T1/2):  1.649

ADMET: Toxicity

hERG Blockers:  0.128 hERG Blockers (10um):  0.274
Human Hepatotoxicity (H-HT):  0.608 Drug-induced Liver Injury (DILI):  0.796
AMES Toxicity:  0.72 Rat Oral Acute Toxicity:  0.234
Maximum Recommended Daily Dose:  0.09 Skin Sensitization:  0.811
Carcinogencity:  0.498 Eye Corrosion:  0.0
Eye Irritation:  0.039 Respiratory Toxicity:  0.247
Drug-induced Neurotoxicity:  0.764 Ototoxicity:  0.974
Hematotoxicity:  0.216 Drug-induced Nephrotoxicity:  0.365
Genotoxicity:  0.988 RPMI-8226 Immunitoxicity:  0.082
A549 Cytotoxicity:  0.048 Hek293 Cytotoxicity:  0.208
BCF:   0.08
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   2.129
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.853
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.805
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. DOI[10.1007/s11306-014-0728-9]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1038/sdata.2014.29]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[11171227]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12576668]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. seed n.a. PMID[25891114]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. Database[MetaboLights]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21080 Solanum lycopersicum Species Solanaceae 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 NPC329209 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
0.8 Intermediate Similarity NPC239737
0.7538 Intermediate Similarity NPC605318
0.5735 Remote Similarity NPC156461
0.5735 Remote Similarity NPC107374
0.5735 Remote Similarity NPC600382
0.5735 Remote Similarity NPC612067
0.5441 Remote Similarity NPC317821
0.5375 Remote Similarity NPC250178
0.5125 Remote Similarity NPC195140

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC329209 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
0.6081 Remote Similarity NPD1750 Clinical (unspecified phase)
0.5867 Remote Similarity NPD1369 Phase 2
0.5735 Remote Similarity NPD249 Phase 4
0.5735 Remote Similarity NPD250 Phase 4
0.5443 Remote Similarity NPD2965 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