Structure

Physi-Chem Properties

Molecular Weight:  131.04
Volume:  128.059
LogP:  0.769
LogD:  1.059
LogS:  -1.728
# Rotatable Bonds:  3
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.556
Synthetic Accessibility Score:  3.363
Fsp3:  0.4
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:  -4.494
MDCK Permeability:  1.4341851965582464e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.985
Plasma Protein Binding (PPB):  22.782365798950195%
Volume Distribution (VD):  0.762
Pgp-substrate:  74.86083221435547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.68
CYP1A2-substrate:  0.621
CYP2C19-inhibitor:  0.196
CYP2C19-substrate:  0.237
CYP2C9-inhibitor:  0.04
CYP2C9-substrate:  0.907
CYP2D6-inhibitor:  0.024
CYP2D6-substrate:  0.65
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.148

ADMET: Excretion

Clearance (CL):  6.394
Half-life (T1/2):  0.896

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.142
Drug-inuced Liver Injury (DILI):  0.154
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.606
Maximum Recommended Daily Dose:  0.032
Skin Sensitization:  0.862
Carcinogencity:  0.182
Eye Corrosion:  0.49
Eye Irritation:  0.968
Respiratory Toxicity:  0.251

Download Data

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

  Natural Product: NPC145077

Natural Product ID:  NPC145077
Common Name*:   Penangin
IUPAC Name:   (E)-N-methyl-3-methylsulfanylprop-2-enamide
Synonyms:   Penangin
Standard InCHIKey:  VRYCXSSOSLPIDH-ONEGZZNKSA-N
Standard InCHI:  InChI=1S/C5H9NOS/c1-6-5(7)3-4-8-2/h3-4H,1-2H3,(H,6,7)/b4-3+
SMILES:  CS/C=C/C(=NC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL505585
PubChem CID:   10419217
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0004020] Vinylogous thioesters

*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
NPO33498 glycosmis sp. Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[9036182]

☑ 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
NPT776 Organism Spodoptera littoralis Spodoptera littoralis EC50 = 0.84 umol/g PMID[459665]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis LC50 > 10.0 umol/g PMID[459665]
NPT1780 Organism Davidiella tassiana Davidiella tassiana ED50 > 200.0 ug ml-1 PMID[459665]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis LC50 = 2.84 umol/dm'2 PMID[459665]

☑ 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 NPC145077 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
0.8605 High Similarity NPC282097
0.6491 Remote Similarity NPC324077
0.641 Remote Similarity NPC32955
0.6222 Remote Similarity NPC205586
0.6042 Remote Similarity NPC470439
0.6042 Remote Similarity NPC86121
0.5962 Remote Similarity NPC267692
0.5962 Remote Similarity NPC307435
0.5849 Remote Similarity NPC243539
0.5849 Remote Similarity NPC54542
0.5849 Remote Similarity NPC304223
0.5849 Remote Similarity NPC267340
0.5849 Remote Similarity NPC145032
0.5818 Remote Similarity NPC314800
0.5741 Remote Similarity NPC195986
0.5636 Remote Similarity NPC303672
0.5636 Remote Similarity NPC119655

  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 NPC145077 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
0.6087 Remote Similarity NPD58 Approved
0.6087 Remote Similarity NPD8806 Approved
0.5714 Remote Similarity NPD8869 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