Natural Product: NPC297753

Natural Product IDNPC297753
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZZLHPCSGGOGHFW-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 82142
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
              • [CHEMONTID:0002404] Alpha amino acids

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 ZZLHPCSGGOGHFW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C4H9NO3S/c1-9(8)2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)
SMILES CS(=O)CC(C(=O)O)N

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   151.03 Volume:   130.98
?
Van der Waals volume.
Dense:   1.153 LogP:   -2.835
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.161
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.28
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   1.0
TPSA:   86.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.495 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.768 Fsp3:   0.75
MCE-18:   3.0
?
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:   0.112 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.042
?
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:   0.712 Promiscuous compounds:   0.446

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.51 MDCK Permeability:   -3.28
Pgp-inhibitor:   0.0 Pgp-substrate:   0.001
PAMPA:   0.995
?
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):   0.003
20% Bioavailability (F20%):   0.004 30% Bioavailability (F30%):   0.008
50% Bioavailability (F50%):   0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.003 MRP1:   0.642
Plasma Protein Binding (PPB):   16.189% Volume Distribution (VD):   -0.272
Fu: 86.374%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.004
OATP1B3 inhibitor:   0.086 BCRP inhibitor:   0.0
BSEP inhibitor:   0.021

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.009 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.072 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.009
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.07
HLM stability:   0.003
?
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):  1.452 Half-life (T1/2):  2.646

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.02
Human Hepatotoxicity (H-HT):  0.566 Drug-induced Liver Injury (DILI):  0.074
AMES Toxicity:  0.735 Rat Oral Acute Toxicity:  0.497
Maximum Recommended Daily Dose:  0.808 Skin Sensitization:  0.999
Carcinogencity:  0.775 Eye Corrosion:  0.386
Eye Irritation:  0.934 Respiratory Toxicity:  0.752
Drug-induced Neurotoxicity:  0.01 Ototoxicity:  0.069
Hematotoxicity:  0.064 Drug-induced Nephrotoxicity:  0.295
Genotoxicity:  0.998 RPMI-8226 Immunitoxicity:  0.037
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.063
BCF:   0.233
?
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:   2.734
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.875
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.214
?
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
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2020.113007]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.3923/pjbs.2013.1138.1144]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[16748484]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[17262437]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18326559]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[20597533]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Essential oil n.a. n.a. PMID[23163425]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23656415]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23865201]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[24508058]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota garlic skin n.a. n.a. PMID[25726329]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[37241721]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23230 Allium cepa Species Amaryllidaceae 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 NPC297753 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
0.7 Intermediate Similarity NPC63621
0.7 Intermediate Similarity NPC326992
0.7 Intermediate Similarity NPC121517
0.7 Intermediate Similarity NPC168375
0.7 Intermediate Similarity NPC600066
0.6818 Remote Similarity NPC245027
0.6818 Remote Similarity NPC162620
0.6818 Remote Similarity NPC62045
0.6364 Remote Similarity NPC118459
0.6364 Remote Similarity NPC309658
0.6364 Remote Similarity NPC327698
0.6364 Remote Similarity NPC53449
0.6316 Remote Similarity NPC116709
0.6316 Remote Similarity NPC21290
0.6316 Remote Similarity NPC272614
0.619 Remote Similarity NPC132307
0.619 Remote Similarity NPC126925
0.6087 Remote Similarity NPC84636
0.6087 Remote Similarity NPC226027
0.6087 Remote Similarity NPC174246
0.6087 Remote Similarity NPC43204
0.5769 Remote Similarity NPC102815
0.5714 Remote Similarity NPC82239
0.5652 Remote Similarity NPC329263
0.5652 Remote Similarity NPC604272
0.5652 Remote Similarity NPC607953
0.56 Remote Similarity NPC167986
0.56 Remote Similarity NPC291186
0.56 Remote Similarity NPC600338
0.5484 Remote Similarity NPC487693
0.5417 Remote Similarity NPC601942
0.5385 Remote Similarity NPC608987
0.52 Remote Similarity NPC49952
0.52 Remote Similarity NPC153370
0.52 Remote Similarity NPC34908
0.52 Remote Similarity NPC136476
0.5185 Remote Similarity NPC602457

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC297753 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
0.6818 Remote Similarity NPD9018 Phase 3
0.6316 Remote Similarity NPD8210 Phase 3
0.6316 Remote Similarity NPD8211 Approved
0.619 Remote Similarity NPD8798 Phase 2
0.6087 Remote Similarity NPD9017 Phase 2
0.6 Remote Similarity NPD9021 Pre-clinical
0.56 Remote Similarity NPD8804 Phase 4
0.56 Remote Similarity NPD8805 Approved
0.56 Remote Similarity NPD9016 Phase 1
0.52 Remote Similarity NPD8614 Pre-clinical

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