NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	164.07
Volume:	158.1
LogP:	-2.989
LogD:	-0.824
LogS:	-0.995
# Rotatable Bonds:	4
TPSA:	63.32
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.559
Synthetic Accessibility Score:	3.671
Fsp3:	0.833
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:	-5.873
MDCK Permeability:	0.00012843208969570696
Pgp-inhibitor:	0.0
Pgp-substrate:	0.94
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.773
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.18
Plasma Protein Binding (PPB):	19.807781219482422%
Volume Distribution (VD):	0.721
Pgp-substrate:	80.08124542236328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.059
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.095
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.207
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.203
CYP3A4-inhibitor:	0.011
CYP3A4-substrate:	0.065

ADMET: Excretion

Clearance (CL):	2.871
Half-life (T1/2):	0.843

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.047
Drug-inuced Liver Injury (DILI):	0.006
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.077
Carcinogencity:	0.371
Eye Corrosion:	0.004
Eye Irritation:	0.034
Respiratory Toxicity:	0.047

Download Data

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

Natural Product: NPC489880

Natural Product ID:	NPC489880
*Common Name:**	S-Methyl-L-methionine chloride
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MYGVPKMVGSXPCQ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C6H13NO2S.ClH/c1-10(2)4-3-5(7)6(8)9;/h5H,3-4,7H2,1-2H3;1H
SMILES:	[Cl-].C[S+](C)CCC(N)C(O)=O
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: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:0004143] Methionine 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
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24014097]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24128451]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7576	Brassica oleracea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7576	Brassica oleracea	Species	Brassicaceae	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
NPO7576	NPC489880	Raw	Leaf	1.35	0.2	2.5	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

☑ 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 NPC489880 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 NPC489880 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