Structure

Physi-Chem Properties

Molecular Weight:  223.05
Volume:  206.169
LogP:  1.11
LogD:  0.789
LogS:  -2.347
# Rotatable Bonds:  1
TPSA:  106.69
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.582
Synthetic Accessibility Score:  3.899
Fsp3:  0.1
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.035
MDCK Permeability:  1.3401499927567784e-05
Pgp-inhibitor:  0.03
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.06
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.038
Plasma Protein Binding (PPB):  88.62227630615234%
Volume Distribution (VD):  0.75
Pgp-substrate:  11.110089302062988%

ADMET: Metabolism

CYP1A2-inhibitor:  0.268
CYP1A2-substrate:  0.799
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.167
CYP2C9-substrate:  0.628
CYP2D6-inhibitor:  0.15
CYP2D6-substrate:  0.326
CYP3A4-inhibitor:  0.058
CYP3A4-substrate:  0.064

ADMET: Excretion

Clearance (CL):  5.089
Half-life (T1/2):  0.933

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.919
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.083
Rat Oral Acute Toxicity:  0.854
Maximum Recommended Daily Dose:  0.131
Skin Sensitization:  0.806
Carcinogencity:  0.864
Eye Corrosion:  0.036
Eye Irritation:  0.625
Respiratory Toxicity:  0.673

Download Data

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

  Natural Product: NPC185928

Natural Product ID:  NPC185928
Common Name*:   Pyranonigrin A
IUPAC Name:   (2R)-2,6-dihydroxy-5-[(E)-prop-1-enyl]-1,2-dihydropyrano[3,2-b]pyrrole-3,7-dione
Synonyms:  
Standard InCHIKey:  JHRSKIPBFMBFDI-VMZHVLLKSA-N
Standard InCHI:  InChI=1S/C10H9NO5/c1-2-3-4-6(12)7(13)5-9(16-4)8(14)10(15)11-5/h2-3,10-12,15H,1H3/b3-2+/t10-/m1/s1
SMILES:  C/C=C/c1oc2C(=O)[C@H](Nc2c(=O)c1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452363
PubChem CID:   11379075
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0003671] Aryl alkyl ketones

*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
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)88611-1]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np058103o]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/JR9620000040]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1966.10858561]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1972.10860562]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. DOI[10.1080/00021369.1985.10867263]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[10695672]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12458767]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12542363]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15387655]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. sponge-derived n.a. PMID[15387655]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15556711]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15620260]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17653510]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17827758]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20014861]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20028011]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21176790]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21543515]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[21774474]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. latex n.a. PMID[21854017]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21854017]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22921072]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24684908]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25044953]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25062661]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25293978]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26040782]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26132344]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26414728]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[27245874]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[32159958]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[6073032]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. mycelium n.a. Database[Article]
NPO14234 Aspergillus niger Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO14234 Aspergillus niger Species Aspergillaceae 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
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 29.0 % PMID[490481]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 85.0 % PMID[490481]

☑ 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 NPC185928 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
0.6404 Remote Similarity NPC326126
0.6042 Remote Similarity NPC312419
0.6022 Remote Similarity NPC263266
0.5926 Remote Similarity NPC313234
0.5682 Remote Similarity NPC475618
0.5644 Remote Similarity NPC296589

  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 NPC185928 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
0.5876 Remote Similarity NPD5115 Clinical (unspecified phase)
0.5833 Remote Similarity NPD9306 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