Natural Product: NPC513331

Natural Product IDNPC513331
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-(2-aminovinyl)-1~{H}-indol-5-ol
IUPAC Name 3-(2-aminovinyl)-1~{H}-indol-5-ol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
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 JGSAFKIGYSSCAA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C10H10N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-6,12-13H,11H2
SMILES NC=CC1=CNC2=CC=C(O)C=C12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   174.08 Volume:   182.005
?
Van der Waals volume.
Dense:   0.956 LogP:   0.629
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.933
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.251
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   11.0
TPSA:   62.04
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.617 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.769 Fsp3:   0.0
MCE-18:   10.0
?
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:   0.599 Fluc inhibitor:   0.155
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.478
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.304
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.391 Promiscuous compounds:   0.91

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.949 MDCK Permeability:   -4.884
Pgp-inhibitor:   0.005 Pgp-substrate:   0.452
PAMPA:   0.501
?
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):   0.008
20% Bioavailability (F20%):   0.136 30% Bioavailability (F30%):   0.321
50% Bioavailability (F50%):   0.755

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.383 MRP1:   0.471
Plasma Protein Binding (PPB):   45.371% Volume Distribution (VD):   0.329
Fu: 50.298%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.731
OATP1B3 inhibitor:   0.921 BCRP inhibitor:   0.075
BSEP inhibitor:   0.034

ADMET: Metabolism

CYP1A2-inhibitor:   0.04 CYP1A2-substrate:   0.019
CYP2C19-inhibitor:   0.096 CYP2C19-substrate:   0.008
CYP2C9-inhibitor:   0.763 CYP2C9-substrate:   0.259
CYP2D6-inhibitor:   0.999 CYP2D6-substrate:   0.023
CYP3A4-inhibitor:   0.018 CYP3A4-substrate:   0.072
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.993
HLM stability:   0.854
?
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):  11.055 Half-life (T1/2):  1.246

ADMET: Toxicity

hERG Blockers:  0.142 hERG Blockers (10um):  0.552
Human Hepatotoxicity (H-HT):  0.554 Drug-induced Liver Injury (DILI):  0.275
AMES Toxicity:  0.851 Rat Oral Acute Toxicity:  0.584
Maximum Recommended Daily Dose:  0.57 Skin Sensitization:  0.696
Carcinogencity:  0.738 Eye Corrosion:  0.017
Eye Irritation:  0.981 Respiratory Toxicity:  0.845
Drug-induced Neurotoxicity:  0.939 Ototoxicity:  0.39
Hematotoxicity:  0.212 Drug-induced Nephrotoxicity:  0.179
Genotoxicity:  0.946 RPMI-8226 Immunitoxicity:  0.064
A549 Cytotoxicity:  0.105 Hek293 Cytotoxicity:  0.374
BCF:   1.19
?
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:   3.602
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.511
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.019
?
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
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jplph.2011.12.019]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1093/jxb/erx356]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. PMID[11575946]
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. PMID[12141860]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. PMID[36447306]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[37980871]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. PMID[39696148]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33241 Bufo gargarizans Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31404 Bufo melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8733 Duttaphrynus melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18994 Mucuna pruriens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO549.1 Musa paradisiaca var. sapientum Varieties Musaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18994 Mucuna pruriens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31404 Bufo melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO549.1 Musa paradisiaca var. sapientum Varieties Musaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18994 Mucuna pruriens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8733 Duttaphrynus melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18994 Mucuna pruriens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31404 Bufo melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8733 Duttaphrynus melanostictus Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18994 Mucuna pruriens Species Fabaceae 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 NPC513331 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
0.6 Remote Similarity NPC220765
0.5909 Remote Similarity NPC171787
0.5909 Remote Similarity NPC276657
0.5652 Remote Similarity NPC74360
0.551 Remote Similarity NPC204717
0.5417 Remote Similarity NPC219087
0.5306 Remote Similarity NPC611528
0.52 Remote Similarity NPC213308
0.52 Remote Similarity NPC171171
0.5098 Remote Similarity NPC32771
0.5094 Remote Similarity NPC45459
0.5094 Remote Similarity NPC315491

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC513331 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
0.5094 Remote Similarity NPD484 Phase 4

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