Structure

Physi-Chem Properties

Molecular Weight:  209.97
Volume:  181.096
LogP:  2.297
LogD:  2.711
LogS:  -4.961
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.353
Synthetic Accessibility Score:  4.11
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.732
MDCK Permeability:  2.3578681066283025e-05
Pgp-inhibitor:  0.139
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.982
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  74.94947052001953%
Volume Distribution (VD):  0.891
Pgp-substrate:  5.188326835632324%

ADMET: Metabolism

CYP1A2-inhibitor:  0.92
CYP1A2-substrate:  0.887
CYP2C19-inhibitor:  0.99
CYP2C19-substrate:  0.837
CYP2C9-inhibitor:  0.924
CYP2C9-substrate:  0.894
CYP2D6-inhibitor:  0.184
CYP2D6-substrate:  0.886
CYP3A4-inhibitor:  0.666
CYP3A4-substrate:  0.416

ADMET: Excretion

Clearance (CL):  10.225
Half-life (T1/2):  0.105

ADMET: Toxicity

hERG Blockers:  0.068
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.946
Rat Oral Acute Toxicity:  0.431
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.971
Carcinogencity:  0.481
Eye Corrosion:  0.991
Eye Irritation:  0.993
Respiratory Toxicity:  0.984

Download Data

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

  Natural Product: NPC85637

Natural Product ID:  NPC85637
Common Name*:   RMKCQUWJDRTEHE-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RMKCQUWJDRTEHE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H10S4/c1-3-5-7-9-10-8-6-4-2/h3-4H,1-2,5-6H2
SMILES:  C=CCSSSSCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   75552
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0004195] Allyl sulfur compounds

*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]
NPO17213 Carya illinoinensis Species Juglandaceae 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 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]
NPO17213 Carya illinoinensis Species Juglandaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23493 Zanthoxylum dissitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO17213 Carya illinoinensis Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23493 Zanthoxylum dissitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2055 Berberis integerrima Species Berberidaceae 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]
NPO23493 Zanthoxylum dissitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17213 Carya illinoinensis Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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]

☑ 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
NPT35 Others n.a. LogP = 3.12 n.a. PMID[468111]

☑ 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 NPC85637 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 NPC85637 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