Natural Product: NPC12100

Natural Product IDNPC12100
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Clathridine
IUPAC Name 5-[[4-(1,3-benzodioxol-5-ylmethyl)-1-methylimidazol-2-yl]amino]-3-methylimidazole-2,4-dione
Synonyms Clathridine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1173467
PubChem CID 364701
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino 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 DNQGARKMDHLOGM-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H15N5O4/c1-20-7-10(5-9-3-4-11-12(6-9)25-8-24-11)17-15(20)18-13-14(22)21(2)16(23)19-13/h3-4,6-7H,5,8H2,1-2H3,(H,17,18,19,23)
SMILES OC1=NC(=Nc2nc(cn2C)Cc2ccc3c(c2)OCO3)C(=O)N1C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   341.11 Volume:   320.119
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Van der Waals volume.
Dense:   1.066 LogP:   0.218
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.675
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.593
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The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   22.0
TPSA:   101.54
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.902 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.362 Fsp3:   0.25
MCE-18:   46.2
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.499 Fluc inhibitor:   0.256
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.5
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.548
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.006 Promiscuous compounds:   0.004

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.044 MDCK Permeability:   -4.679
Pgp-inhibitor:   0.083 Pgp-substrate:   0.01
PAMPA:   0.606
?
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):   0.061
20% Bioavailability (F20%):   0.647 30% Bioavailability (F30%):   0.072
50% Bioavailability (F50%):   0.787

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.764 MRP1:   0.756
Plasma Protein Binding (PPB):   94.368% Volume Distribution (VD):   0.035
Fu: 6.092%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.938
OATP1B3 inhibitor:   0.636 BCRP inhibitor:   0.0
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.999 CYP1A2-substrate:   0.006
CYP2C19-inhibitor:   0.812 CYP2C19-substrate:   0.006
CYP2C9-inhibitor:   0.725 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.169 CYP2D6-substrate:   0.925
CYP3A4-inhibitor:   0.995 CYP3A4-substrate:   0.019
CYP2B6-substrate:   0.003 CYP2C8-inhibitor:   0.0
HLM stability:   0.121
?
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):  2.355 Half-life (T1/2):  1.178

ADMET: Toxicity

hERG Blockers:  0.042 hERG Blockers (10um):  0.108
Human Hepatotoxicity (H-HT):  0.989 Drug-induced Liver Injury (DILI):  0.997
AMES Toxicity:  0.956 Rat Oral Acute Toxicity:  0.669
Maximum Recommended Daily Dose:  0.603 Skin Sensitization:  0.996
Carcinogencity:  0.983 Eye Corrosion:  0.0
Eye Irritation:  0.083 Respiratory Toxicity:  0.486
Drug-induced Neurotoxicity:  0.349 Ototoxicity:  0.62
Hematotoxicity:  0.699 Drug-induced Nephrotoxicity:  0.882
Genotoxicity:  0.999 RPMI-8226 Immunitoxicity:  0.03
A549 Cytotoxicity:  0.005 Hek293 Cytotoxicity:  0.228
BCF:   0.831
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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:   3.441
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.915
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.303
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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
NPO19556 Clathrina clathrus Species Clathrinidae Eukaryota n.a. n.a. n.a. PMID[20590100]
NPO19556 Clathrina clathrus Species Clathrinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19556 Clathrina clathrus Species Clathrinidae 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
NPT83 Cell line MCF7 Homo sapiens IC50 > 100000.0 nM PMID[28159485]
NPT20 Organism Candida albicans Candida albicans IZ = 18.0 mm DOI[10.1039/C3MD00097D]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 0.0 mm DOI[10.1039/C3MD00097D]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm DOI[10.1039/C3MD00097D]

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 NPC12100 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
0.6438 Remote Similarity NPC308906
0.5676 Remote Similarity NPC17305
0.5676 Remote Similarity NPC489314
0.5375 Remote Similarity NPC242923

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC12100 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