Structure

Physi-Chem Properties

Molecular Weight:  213.99
Volume:  178.562
LogP:  0.785
LogD:  0.888
LogS:  -2.09
# Rotatable Bonds:  1
TPSA:  49.74
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.475
Synthetic Accessibility Score:  5.112
Fsp3:  0.286
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.981
MDCK Permeability:  5.2214149945939425e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.128
20% Bioavailability (F20%):  0.033
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.99
Plasma Protein Binding (PPB):  45.152252197265625%
Volume Distribution (VD):  0.8
Pgp-substrate:  29.525352478027344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.626
CYP1A2-substrate:  0.849
CYP2C19-inhibitor:  0.694
CYP2C19-substrate:  0.754
CYP2C9-inhibitor:  0.616
CYP2C9-substrate:  0.735
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.491
CYP3A4-inhibitor:  0.075
CYP3A4-substrate:  0.711

ADMET: Excretion

Clearance (CL):  7.81
Half-life (T1/2):  0.527

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.038
Drug-inuced Liver Injury (DILI):  0.771
AMES Toxicity:  0.835
Rat Oral Acute Toxicity:  0.883
Maximum Recommended Daily Dose:  0.046
Skin Sensitization:  0.913
Carcinogencity:  0.193
Eye Corrosion:  0.041
Eye Irritation:  0.294
Respiratory Toxicity:  0.981

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

  Natural Product: NPC477864

Natural Product ID:  NPC477864
Common Name*:   Formylpyrrothine
IUPAC Name:   N-(4-methyl-5-oxodithiolo[4,3-b]pyrrol-6-yl)formamide
Synonyms:   Formylpyrrothine
Standard InCHIKey:  JSPVCJSCSHLERJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H6N2O2S2/c1-9-4-2-12-13-6(4)5(7(9)11)8-3-10/h2-3H,1H3,(H,8,10)
SMILES:  CN1C2=CSSC2=C(C1=O)NC=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   46848162
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0003282] N-arylamides

*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
NPO33537 Saccharothrix algeriensis Species Pseudonocardiaceae Bacteria isolated from a Saharan soil sample Adrar, southwest of Algeria 1992 PMID[20507156]

☑ 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
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 2 ug/ml PMID[20507156]
NPT1823 Organism Bacillus coagulans Bacillus coagulans MIC = 2 ug/ml PMID[20507156]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 2 ug/ml PMID[20507156]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC = 3 ug/ml PMID[20507156]
NPT3086 Organism Penicillium expansum Penicillium expansum MIC = 3 ug/ml PMID[20507156]
NPT5959 Organism Umbelopsis ramanniana Umbelopsis ramanniana MIC = 10 ug/ml PMID[20507156]
NPT3685 Organism Fusarium equiseti Fusarium equiseti MIC = 10 ug/ml PMID[20507156]
NPT1278 Organism Fusarium culmorum Fusarium culmorum MIC = 10 ug/ml PMID[20507156]
NPT564 Organism Listeria monocytogenes Listeria monocytogenes MIC = 20 ug/ml PMID[20507156]
NPT637 Organism Fusarium oxysporum Fusarium oxysporum MIC = 30 ug/ml PMID[20507156]
NPT19 Organism Escherichia coli Escherichia coli MIC = 40 ug/ml PMID[20507156]
NPT1276 Organism Gibberella zeae Gibberella zeae MIC = 40 ug/ml PMID[20507156]
NPT2 Others Unspecified MIC = 50 ug/ml PMID[20507156]
NPT4083 Organism Gibberella fujikuroi Gibberella fujikuroi MIC = 75 ug/ml PMID[20507156]
NPT20 Organism Candida albicans Candida albicans MIC = 75 ug/ml PMID[20507156]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 75 ug/ml PMID[20507156]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC > 100 ug/ml PMID[20507156]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC > 100 ug/ml PMID[20507156]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 100 ug/ml PMID[20507156]
NPT141 Organism Agrobacterium tumefaciens Agrobacterium tumefaciens MIC > 100 ug/ml PMID[20507156]

☑ 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 NPC477864 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
0.8923 High Similarity NPC40598
0.8657 High Similarity NPC316309
0.8286 Intermediate Similarity NPC477862
0.8169 Intermediate Similarity NPC477863
0.6324 Remote Similarity NPC314800

  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 NPC477864 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