Structure

Physi-Chem Properties

Molecular Weight:  106.01
Volume:  93.897
LogP:  0.427
LogD:  -0.369
LogS:  -0.019
# Rotatable Bonds:  2
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.5
Synthetic Accessibility Score:  2.654
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.452
MDCK Permeability:  0.00012735016935039312
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.07
20% Bioavailability (F20%):  0.019
30% Bioavailability (F30%):  0.19

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.03
Plasma Protein Binding (PPB):  78.40599060058594%
Volume Distribution (VD):  0.264
Pgp-substrate:  35.401390075683594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.788
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.236
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  10.166
Half-life (T1/2):  0.888

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.395
Drug-inuced Liver Injury (DILI):  0.249
AMES Toxicity:  0.796
Rat Oral Acute Toxicity:  0.857
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.236
Carcinogencity:  0.757
Eye Corrosion:  0.952
Eye Irritation:  0.985
Respiratory Toxicity:  0.361

Download Data

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

  Natural Product: NPC320704

Natural Product ID:  NPC320704
Common Name*:   Mercaptopropionic Acid
IUPAC Name:   3-sulfanylpropanoic acid
Synonyms:   Mercaptopropionic Acid
Standard InCHIKey:  DKIDEFUBRARXTE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H6O2S/c4-3(5)1-2-6/h6H,1-2H2,(H,4,5)
SMILES:  C(CS)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL358697
PubChem CID:   6514
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001205] Carboxylic acids

*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
NPO30560 Thalassiosira pseudonana Species Thalassiosiraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]

☑ 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
NPT567 Individual Protein Matrix metalloproteinase 3 Homo sapiens Kd = 3000000.0 nM PMID[512982]
NPT5053 Individual Protein Beta-lactamase Pseudomonas aeruginosa Ki = 180.0 nM PMID[512986]
NPT317 Uncleic Acid Nucleic Acid Cleavage = 52.3 % PMID[512983]
NPT317 Uncleic Acid Nucleic Acid Cleavage = 78.9 % PMID[512983]
NPT2 Others Unspecified IC50 = 170000.0 nM PMID[512984]
NPT32 Organism Mus musculus Mus musculus ED50 = 17.1 mg.kg-1 PMID[512985]
NPT2 Others Unspecified INH = 1.2 uM PMID[512987]
NPT2 Others Unspecified Potency n.a. 49938.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19880.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 78448.2 nM PubChem BioAssay data set

☑ 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 NPC320704 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
0.8276 Intermediate Similarity NPC16947
0.7742 Intermediate Similarity NPC14778
0.7308 Intermediate Similarity NPC181153
0.7 Intermediate Similarity NPC319333
0.6579 Remote Similarity NPC317691
0.6579 Remote Similarity NPC254482
0.6579 Remote Similarity NPC110533
0.6579 Remote Similarity NPC326808
0.6486 Remote Similarity NPC329545
0.6333 Remote Similarity NPC230726
0.6333 Remote Similarity NPC314668
0.6333 Remote Similarity NPC3343
0.6333 Remote Similarity NPC286233
0.6333 Remote Similarity NPC149209
0.6154 Remote Similarity NPC68873
0.5952 Remote Similarity NPC248970
0.5952 Remote Similarity NPC306238
0.5952 Remote Similarity NPC49952
0.5952 Remote Similarity NPC136476
0.5938 Remote Similarity NPC236709
0.5758 Remote Similarity NPC122768
0.5758 Remote Similarity NPC151140
0.5758 Remote Similarity NPC61066
0.5758 Remote Similarity NPC292641
0.5758 Remote Similarity NPC174368
0.5758 Remote Similarity NPC104195
0.5714 Remote Similarity NPC85721

  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 NPC320704 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
0.7812 Intermediate Similarity NPD8596 Approved
0.7576 Intermediate Similarity NPD8597 Approved
0.7308 Intermediate Similarity NPD8201 Phase 2
0.6875 Remote Similarity NPD8595 Approved
0.6579 Remote Similarity NPD8215 Approved
0.6579 Remote Similarity NPD8214 Approved
0.6333 Remote Similarity NPD8189 Approved
0.6154 Remote Similarity NPD7364 Approved
0.6154 Remote Similarity NPD8200 Phase 2
0.6 Remote Similarity NPD8231 Approved
0.5952 Remote Similarity NPD8870 Approved
0.5938 Remote Similarity NPD8593 Approved
0.5938 Remote Similarity NPD8594 Approved
0.5854 Remote Similarity NPD8869 Approved
0.5758 Remote Similarity NPD8619 Approved
0.5758 Remote Similarity NPD8617 Approved
0.5682 Remote Similarity NPD9214 Phase 3
0.5682 Remote Similarity NPD9213 Approved

  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