NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	234.02
Volume:	220.628
LogP:	0.824
LogD:	0.587
LogS:	-2.101
# Rotatable Bonds:	8
TPSA:	23.06
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.279
Synthetic Accessibility Score:	5.586
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.94
MDCK Permeability:	2.357060475333128e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.015
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	82.50980377197266%
Volume Distribution (VD):	1.05
Pgp-substrate:	4.232032775878906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.079
CYP1A2-substrate:	0.446
CYP2C19-inhibitor:	0.452
CYP2C19-substrate:	0.704
CYP2C9-inhibitor:	0.182
CYP2C9-substrate:	0.897
CYP2D6-inhibitor:	0.632
CYP2D6-substrate:	0.898
CYP3A4-inhibitor:	0.662
CYP3A4-substrate:	0.237

ADMET: Excretion

Clearance (CL):	9.244
Half-life (T1/2):	0.951

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.088
Drug-inuced Liver Injury (DILI):	0.541
AMES Toxicity:	0.974
Rat Oral Acute Toxicity:	0.179
Maximum Recommended Daily Dose:	0.275
Skin Sensitization:	0.947
Carcinogencity:	0.905
Eye Corrosion:	0.964
Eye Irritation:	0.988
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC164498

Natural Product ID:	NPC164498
*Common Name:**	IXELFRRANAOWSF-SCXUMTSISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IXELFRRANAOWSF-SCXUMTSISA-N
Standard InCHI:	InChI=1S/C9H14OS3/c1-3-6-11-12-7-5-9-13(10)8-4-2/h3-5,7H,1-2,6,8-9H2/b7-5-/t13-/m0/s1
SMILES:	C=CCSS/C=CC[S@@](=O)CC=C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	76960957
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000004] Organosulfur compounds [CHEMONTID:0000491] Sulfoxides

*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.	fruit	n.a.	PMID[24467533]
NPO3186	Loranthus parasiticus	Species	Loranthaceae	Eukaryota	n.a.	n.a.	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	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	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	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]
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]
NPO7103	Allium sativum	Species	Amaryllidaceae	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]
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]
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]

☑ 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 NPC164498 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	22462
0.1-0.2	18908
0.2-0.3	1163
0.3-0.4	128
0.4-0.5	21
0.5-0.6	5
0.6-0.7	5
0.7-0.8	1
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	2

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 NPC164498 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	5010
0.1-0.2	3873
0.2-0.3	241
0.3-0.4	16
0.4-0.5	10
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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