Structure

Physi-Chem Properties

Molecular Weight:  127.94
Volume:  28730949.528
LogP:  -1.349
LogD:  -0.917
LogS:  0.958
# Rotatable Bonds:  0
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.446
Synthetic Accessibility Score:  5.684
Fsp3:  1.0
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:  -4.661
MDCK Permeability:  0.0007689010817557573
Pgp-inhibitor:  0.0
Pgp-substrate:  0.02
Human Intestinal Absorption (HIA):  0.16
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.815

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.711
Plasma Protein Binding (PPB):  8.024443626403809%
Volume Distribution (VD):  0.731
Pgp-substrate:  85.54429626464844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.152
CYP1A2-substrate:  0.695
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.513
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.837
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.597
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.138

ADMET: Excretion

Clearance (CL):  6.372
Half-life (T1/2):  0.746

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.104
Drug-inuced Liver Injury (DILI):  0.241
AMES Toxicity:  0.142
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.062
Skin Sensitization:  0.352
Carcinogencity:  0.272
Eye Corrosion:  0.987
Eye Irritation:  0.993
Respiratory Toxicity:  0.125

Download Data

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

  Natural Product: NPC74400

Natural Product ID:  NPC74400
Common Name*:   Methylseleninic Acid
IUPAC Name:   methaneseleninic acid
Synonyms:   Methylseleninic Acid
Standard InCHIKey:  UEQANLFPOFICBH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/CH4O2Se/c1-4(2)3/h1H3,(H,2,3)
SMILES:  C[Se](=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL399906
PubChem CID:   161597
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0002027] Seleninic acids 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 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]
NPO7103 Allium sativum 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]
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]
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

☑ 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
NPT306 Cell Line PC-3 Homo sapiens IC50 = 8380.0 nM PMID[528503]
NPT83 Cell Line MCF7 Homo sapiens RatioGI50 = 1.4 n.a. PMID[528505]
NPT1307 Cell Line Calu-1 Homo sapiens GI50 = 3540.0 nM PMID[528506]
NPT306 Cell Line PC-3 Homo sapiens GI50 = 2450.0 nM PMID[528506]
NPT83 Cell Line MCF7 Homo sapiens GI50 = 1280.0 nM PMID[528506]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 = 1080.0 nM PMID[528506]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 < 8400.0 nM PMID[528504]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 1800.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 2500.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 1300.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. TGI = 3400.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. LC50 > 100000.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. TGI = 8400.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. LC50 = 37100.0 nM PMID[528505]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. TGI = 3800.0 nM PMID[528505]
NPT24746 CELL-LINE 184B5 Homo sapiens GI50 = 1790.0 nM PMID[528506]
NPT2 Others Unspecified RatioGI50 = 1.4 n.a. PMID[528506]
NPT23095 CELL-LINE BEAS-2B Homo sapiens GI50 = 3660.0 nM PMID[528506]
NPT2 Others Unspecified RatioGI50 = 1.03 n.a. PMID[528506]

☑ 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 NPC74400 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
NPC

  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 NPC74400 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
NPD

  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