Natural Product: NPC83032

Natural Product IDNPC83032
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Isoamylamine
IUPAC Name 3-methylbutan-1-amine
Synonyms 3-Methyl-Butylamine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL42003
PubChem CID 7894
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002450] Primary amines
            • [CHEMONTID:0000469] Monoalkylamines

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 BMFVGAAISNGQNM-UHFFFAOYSA-N
Standard InCHI InChI=1S/C5H13N/c1-5(2)3-4-6/h5H,3-4,6H2,1-2H3
SMILES CC(C)CCN

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   87.1 Volume:   106.033
?
Van der Waals volume.
Dense:   0.821 LogP:   1.592
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.025
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.738
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   0.0
TPSA:   26.02
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.534 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.153 Fsp3:   1.0
MCE-18:   0.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.078 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.994 Promiscuous compounds:   0.443

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.078 MDCK Permeability:   -5.479
Pgp-inhibitor:   0.007 Pgp-substrate:   0.933
PAMPA:   0.584
?
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):   0.454
20% Bioavailability (F20%):   0.044 30% Bioavailability (F30%):   0.068
50% Bioavailability (F50%):   0.376

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.835 MRP1:   0.35
Plasma Protein Binding (PPB):   10.21% Volume Distribution (VD):   0.427
Fu: 94.485%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.494
OATP1B3 inhibitor:   0.539 BCRP inhibitor:   0.082
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.879 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.281 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.014 CYP2C9-substrate:   0.735
CYP2D6-inhibitor:   0.879 CYP2D6-substrate:   0.01
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.325
CYP2B6-substrate:   0.002 CYP2C8-inhibitor:   0.032
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):  9.708 Half-life (T1/2):  1.137

ADMET: Toxicity

hERG Blockers:  0.253 hERG Blockers (10um):  0.57
Human Hepatotoxicity (H-HT):  0.486 Drug-induced Liver Injury (DILI):  0.043
AMES Toxicity:  0.349 Rat Oral Acute Toxicity:  0.487
Maximum Recommended Daily Dose:  0.248 Skin Sensitization:  0.866
Carcinogencity:  0.313 Eye Corrosion:  0.999
Eye Irritation:  0.987 Respiratory Toxicity:  0.842
Drug-induced Neurotoxicity:  0.668 Ototoxicity:  0.363
Hematotoxicity:  0.279 Drug-induced Nephrotoxicity:  0.274
Genotoxicity:  0.017 RPMI-8226 Immunitoxicity:  0.052
A549 Cytotoxicity:  0.045 Hek293 Cytotoxicity:  0.071
BCF:   0.391
?
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:   2.428
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.487
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.467
?
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
NPO1524 Rosa rugosa Species Rosaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodcont.2014.02.001]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Antalya and Mugla Provinces, Turkey 200-Aug DOI[10.1016/j.scienta.2010.10.027]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. whole plant n.a. PMID[11824569]
NPO19602 Nephelium maingayi Species Sapindaceae Eukaryota bark n.a. n.a. PMID[14987059]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Cork, Ireland n.a. PMID[15223592]
NPO18559 Cucumaria okhotensis Species n.a. n.a. n.a. n.a. n.a. PMID[18288810]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota Flowers n.a. n.a. PMID[20467822]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota flower buds n.a. n.a. PMID[24063567]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota Roots n.a. n.a. PMID[24461297]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26562611]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota Fruits n.a. n.a. PMID[29140705]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[34332066]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[36986275]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19542 Grindelia havardii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18559 Cucumaria okhotensis Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO17557 Hydrodictyon reticulatum Species Hydrodictyaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19214 Polyscias scutellaria Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19474 Clavaria pyxidata Species Clavariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18991 Senecio candollei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19542 Grindelia havardii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19801 Euphorbia armena Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19214 Polyscias scutellaria Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18559 Cucumaria okhotensis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19343 Centaurea glastifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17305 Oenanthe phellandrium Species Muscicapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19602 Nephelium maingayi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1524 Rosa rugosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17557 Hydrodictyon reticulatum Species Hydrodictyaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14500 Pyrus pyraster Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15688 Astragalus oxyphysus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12588 Cornus officinalis Species Cornaceae 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
NPT3968 Individual protein Leucine aminopeptidase Homo sapiens Ki > 50000000.0 nM PMID[3625708]

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
- Rattus norvegicus LD50 = 341.0 mg/kg ToxVal
- Rattus norvegicus LD50 = 520.0 mg/kg ToxVal
- Rattus norvegicus LD50 = 328.0 mg/kg ToxVal
- Rattus norvegicus LD50 = 427.0 mg/kg ToxVal
- Rattus norvegicus LC50 = 13700.0 mg/m3 ToxVal
- Rattus norvegicus LC50 = 8500.0 mg/m3 ToxVal
- Rattus norvegicus LC50 = 11500.0 mg/m3 ToxVal
- Rattus norvegicus LD50 = 2000.0 mg/kg ToxVal
- Mus musculus LD50 = 2.300513645 mg/kg TOXRIC

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 NPC83032 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
0.5833 Remote Similarity NPC27869
0.5455 Remote Similarity NPC309715

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC83032 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