Natural Product: NPC604436

Natural Product IDNPC604436
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ALEPIEAQGFDQEN-DUVUQDDDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL229252
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 ALEPIEAQGFDQEN-DUVUQDDDSA-N
Standard InCHI InChI=1S/C12H25NO/c1-3-4-5-6-7-8-9-10-12(14)11(2)13/h5-6,11-12,14H,3-4,7-10,13H2,1-2H3/b6-5-/t11-,12+/m1/s1
SMILES CCC/C=CCCCC[C@H](O)[C@@H](C)N

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   199.19 Volume:   233.259
?
Van der Waals volume.
Dense:   0.854 LogP:   3.266
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.867
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.751
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   1.0
TPSA:   46.25
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.466 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.27 Fsp3:   0.833
MCE-18:   2.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.352 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.757 Promiscuous compounds:   0.268

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.008 MDCK Permeability:   -4.811
Pgp-inhibitor:   0.375 Pgp-substrate:   0.034
PAMPA:   0.104
?
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):   0.018
20% Bioavailability (F20%):   0.222 30% Bioavailability (F30%):   0.388
50% Bioavailability (F50%):   0.918

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.258 MRP1:   0.894
Plasma Protein Binding (PPB):   85.753% Volume Distribution (VD):   0.003
Fu: 12.291%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.533
OATP1B3 inhibitor:   0.866 BCRP inhibitor:   0.332
BSEP inhibitor:   0.614

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.002
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.938
CYP2D6-inhibitor:   0.999 CYP2D6-substrate:   0.078
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.986
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.954
HLM stability:   0.194
?
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):  6.393 Half-life (T1/2):  1.185

ADMET: Toxicity

hERG Blockers:  0.2 hERG Blockers (10um):  0.382
Human Hepatotoxicity (H-HT):  0.368 Drug-induced Liver Injury (DILI):  0.003
AMES Toxicity:  0.313 Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.051 Skin Sensitization:  1.0
Carcinogencity:  0.047 Eye Corrosion:  0.993
Eye Irritation:  0.969 Respiratory Toxicity:  0.828
Drug-induced Neurotoxicity:  0.118 Ototoxicity:  0.381
Hematotoxicity:  0.03 Drug-induced Nephrotoxicity:  0.298
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.377 Hek293 Cytotoxicity:  0.146
BCF:   1.918
?
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:   4.116
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.199
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.823
?
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
NPO26152 Clavelina oblonga Species Clavelinidae Eukaryota n.a. n.a. n.a. PMID[15568780]
NPO26152 Clavelina oblonga Species Clavelinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26152 Clavelina oblonga Species Clavelinidae 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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity n.a. n.a. n.a. PMID[21955681]

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 NPC604436 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
0.8148 Intermediate Similarity NPC478318
0.6875 Remote Similarity NPC113224
0.6875 Remote Similarity NPC601273
0.6786 Remote Similarity NPC168308
0.6786 Remote Similarity NPC302569
0.6538 Remote Similarity NPC478319
0.6538 Remote Similarity NPC121062
0.6538 Remote Similarity NPC29222
0.6538 Remote Similarity NPC96966
0.6538 Remote Similarity NPC602997
0.6452 Remote Similarity NPC47333
0.64 Remote Similarity NPC474322
0.6129 Remote Similarity NPC603231
0.5758 Remote Similarity NPC485043
0.5625 Remote Similarity NPC485042

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC604436 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
0.6538 Remote Similarity NPD3214 Discontinued

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