Structure

Physi-Chem Properties

Molecular Weight:  136.0
Volume:  120.912
LogP:  0.728
LogD:  -0.109
LogS:  -0.92
# Rotatable Bonds:  3
TPSA:  23.06
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.33
Synthetic Accessibility Score:  5.943
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.703
MDCK Permeability:  4.935203105560504e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.215
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.096

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.792
Plasma Protein Binding (PPB):  63.57386016845703%
Volume Distribution (VD):  0.861
Pgp-substrate:  16.539308547973633%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.485
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.859
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.564
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.768
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  8.854
Half-life (T1/2):  0.796

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.084
Drug-inuced Liver Injury (DILI):  0.132
AMES Toxicity:  0.891
Rat Oral Acute Toxicity:  0.798
Maximum Recommended Daily Dose:  0.108
Skin Sensitization:  0.941
Carcinogencity:  0.878
Eye Corrosion:  0.986
Eye Irritation:  0.995
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC172112

Natural Product ID:  NPC172112
Common Name*:   ZIMQNNOENLFVMT-ZETCQYMHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZIMQNNOENLFVMT-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C4H8OS2/c1-3-4-7(5)6-2/h3H,1,4H2,2H3/t7-/m1/s1
SMILES:  C=CC[S@](=O)SC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001161] Thiosulfinic acid esters

*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]
NPO10434 Rhodospirillum rubrum Species Rhodospirillaceae Bacteria n.a. n.a. n.a. PMID[18826254]
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]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. PMID[24467533]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. fruit n.a. PMID[24467533]
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]
NPO13017 Nauclea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[31429278]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
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]
NPO7103 Allium sativum 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 Bulb n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2055 Berberis integerrima Species Berberidaceae 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]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum 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]
NPO13017 Nauclea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1625 Ovibos moschatus Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11481 Elephantopus angustifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8817 Herbertus sakuraii Species Herbertaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10434 Rhodospirillum rubrum Species Rhodospirillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4177 Libocedrus decurrens Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8146 Aniba megaphylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3186 Loranthus parasiticus Species Loranthaceae 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

☑ 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

☑ 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 NPC172112 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

  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 NPC172112 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

  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