Structure

Physi-Chem Properties

Molecular Weight:  161.05
Volume:  154.146
LogP:  -1.992
LogD:  0.169
LogS:  -1.728
# Rotatable Bonds:  5
TPSA:  63.32
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  3.237
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.628
MDCK Permeability:  6.71496900395141e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.531
Plasma Protein Binding (PPB):  32.967533111572266%
Volume Distribution (VD):  0.408
Pgp-substrate:  59.991580963134766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.074
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.455
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.272
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.059

ADMET: Excretion

Clearance (CL):  8.186
Half-life (T1/2):  0.832

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.009
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.332
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.291
Carcinogencity:  0.301
Eye Corrosion:  0.031
Eye Irritation:  0.199
Respiratory Toxicity:  0.524

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Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC145235

Natural Product ID:  NPC145235
Common Name*:   2-Amino-3-Prop-2-Enylsulfanylpropanoic Acid
IUPAC Name:   2-amino-3-prop-2-enylsulfanylpropanoic acid
Synonyms:  
Standard InCHIKey:  ZFAHNWWNDFHPOH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H11NO2S/c1-2-3-10-4-5(7)6(8)9/h2,5H,1,3-4,7H2,(H,8,9)
SMILES:  C=CCSCC(C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1592541
PubChem CID:   98280
25202793
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:0004313] Cysteine and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  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[10.3923/pjbs.2013.1138.1144]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Essential oil n.a. n.a. PMID[23163425]
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]
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[8350088]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Plant 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 Shoot n.a. n.a. Database[FooDB]
NPO11014 Allium tuberosum 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]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11014 Allium tuberosum 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]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11014 Allium tuberosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7103 Allium sativum 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 NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO7103 NPC145235 Raw Bulb 1 1 1 mg/100g Database [DUKE]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 28183.8 nM PMID[461150]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 39810.7 nM PMID[461150]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC145235 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9423 High Similarity NPC82239
0.84 Intermediate Similarity NPC204364
0.8077 Intermediate Similarity NPC193989
0.8077 Intermediate Similarity NPC152451
0.8077 Intermediate Similarity NPC170739
0.7925 Intermediate Similarity NPC114990
0.7636 Intermediate Similarity NPC317815
0.75 Intermediate Similarity NPC185755
0.75 Intermediate Similarity NPC198196
0.75 Intermediate Similarity NPC49952
0.75 Intermediate Similarity NPC213876
0.75 Intermediate Similarity NPC136476
0.7414 Intermediate Similarity NPC283786
0.74 Intermediate Similarity NPC254482
0.74 Intermediate Similarity NPC326808
0.74 Intermediate Similarity NPC110533
0.74 Intermediate Similarity NPC317691
0.7368 Intermediate Similarity NPC102815
0.6964 Remote Similarity NPC125736
0.6852 Remote Similarity NPC228932
0.6774 Remote Similarity NPC321419
0.6727 Remote Similarity NPC118187
0.6667 Remote Similarity NPC191136
0.6667 Remote Similarity NPC319175
0.6607 Remote Similarity NPC318523
0.6538 Remote Similarity NPC53449
0.6538 Remote Similarity NPC121517
0.6538 Remote Similarity NPC326992
0.6538 Remote Similarity NPC168375
0.64 Remote Similarity NPC21290
0.64 Remote Similarity NPC116709
0.64 Remote Similarity NPC272614
0.6296 Remote Similarity NPC167986
0.6296 Remote Similarity NPC291186
0.6275 Remote Similarity NPC63621
0.625 Remote Similarity NPC248970
0.625 Remote Similarity NPC306238
0.6226 Remote Similarity NPC237525
0.6226 Remote Similarity NPC326212
0.6182 Remote Similarity NPC126925
0.6182 Remote Similarity NPC132307
0.6182 Remote Similarity NPC325097
0.6182 Remote Similarity NPC198301
0.6071 Remote Similarity NPC118459
0.6071 Remote Similarity NPC329263
0.6071 Remote Similarity NPC327698
0.6 Remote Similarity NPC477777
0.5965 Remote Similarity NPC297220
0.5926 Remote Similarity NPC66043
0.5902 Remote Similarity NPC477779
0.5862 Remote Similarity NPC477776
0.5862 Remote Similarity NPC136159
0.5862 Remote Similarity NPC181588
0.5833 Remote Similarity NPC319021
0.5818 Remote Similarity NPC219143
0.5818 Remote Similarity NPC226265
0.58 Remote Similarity NPC14778
0.5789 Remote Similarity NPC285322
0.5789 Remote Similarity NPC208793
0.5769 Remote Similarity NPC9294
0.5763 Remote Similarity NPC140872
0.5763 Remote Similarity NPC153370
0.5763 Remote Similarity NPC93081
0.5735 Remote Similarity NPC289691
0.5714 Remote Similarity NPC314221
0.5714 Remote Similarity NPC60424
0.569 Remote Similarity NPC309658
0.5667 Remote Similarity NPC226027
0.5667 Remote Similarity NPC162620
0.5667 Remote Similarity NPC316231
0.5667 Remote Similarity NPC93888
0.5667 Remote Similarity NPC62045
0.5667 Remote Similarity NPC43204
0.5667 Remote Similarity NPC112890
0.5667 Remote Similarity NPC270805
0.5667 Remote Similarity NPC174246
0.5667 Remote Similarity NPC84636
0.5667 Remote Similarity NPC245027
0.5667 Remote Similarity NPC324825
0.5652 Remote Similarity NPC325597
0.5652 Remote Similarity NPC174304

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC145235 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.86 High Similarity NPD8873 Approved
0.8269 Intermediate Similarity NPD9025 Approved
0.8077 Intermediate Similarity NPD9021 Approved
0.8077 Intermediate Similarity NPD8802 Approved
0.8077 Intermediate Similarity NPD8803 Clinical (unspecified phase)
0.7636 Intermediate Similarity NPD8849 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD9020 Approved
0.75 Intermediate Similarity NPD8982 Approved
0.74 Intermediate Similarity NPD8214 Approved
0.74 Intermediate Similarity NPD8215 Approved
0.7 Intermediate Similarity NPD8848 Approved
0.6607 Remote Similarity NPD8577 Discontinued
0.6545 Remote Similarity NPD8801 Approved
0.64 Remote Similarity NPD8210 Phase 3
0.64 Remote Similarity NPD8211 Approved
0.6324 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6296 Remote Similarity NPD8805 Approved
0.6296 Remote Similarity NPD8804 Approved
0.625 Remote Similarity NPD8870 Approved
0.623 Remote Similarity NPD8971 Approved
0.6182 Remote Similarity NPD8798 Approved
0.6167 Remote Similarity NPD9386 Approved
0.6056 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6034 Remote Similarity NPD9214 Phase 3
0.6034 Remote Similarity NPD9213 Approved
0.5862 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5833 Remote Similarity NPD329 Discontinued
0.5818 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5818 Remote Similarity NPD8216 Approved
0.5789 Remote Similarity NPD8610 Approved
0.5763 Remote Similarity NPD8808 Approved
0.5763 Remote Similarity NPD8614 Approved
0.5763 Remote Similarity NPD8809 Approved
0.5667 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8624 Approved
0.5667 Remote Similarity NPD9018 Approved
0.5667 Remote Similarity NPD9044 Approved
0.5667 Remote Similarity NPD9017 Approved
0.5652 Remote Similarity NPD348 Approved
0.5645 Remote Similarity NPD9420 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8869 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

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