Structure

Physi-Chem Properties

Molecular Weight:  112.02
Volume:  104.941
LogP:  -0.457
LogD:  0.435
LogS:  -0.403
# Rotatable Bonds:  0
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.526
Synthetic Accessibility Score:  2.728
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.46
MDCK Permeability:  1.9549914213712327e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.044
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.304
Plasma Protein Binding (PPB):  74.9363784790039%
Volume Distribution (VD):  0.832
Pgp-substrate:  44.951393127441406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.367
CYP1A2-substrate:  0.182
CYP2C19-inhibitor:  0.086
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.382
CYP2D6-inhibitor:  0.038
CYP2D6-substrate:  0.605
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.16

ADMET: Excretion

Clearance (CL):  11.526
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.12
Drug-inuced Liver Injury (DILI):  0.392
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.802
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.472
Carcinogencity:  0.913
Eye Corrosion:  0.847
Eye Irritation:  0.989
Respiratory Toxicity:  0.961

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC2741

Natural Product ID:  NPC2741
Common Name*:   3-Hydroxypyran-4-One
IUPAC Name:   3-hydroxypyran-4-one
Synonyms:  
Standard InCHIKey:  VEYIMQVTPXPUHA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H4O3/c6-4-1-2-8-3-5(4)7/h1-3,7H
SMILES:  O=c1ccocc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL79857
PubChem CID:   68129
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones 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
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. whole plant n.a. PMID[16079548]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2236 Pyrola rotundifolia Species Ericaceae 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
NPT567 Individual Protein Matrix metalloproteinase 3 Homo sapiens Inhibition = 35.0 % PMID[478661]
NPT568 Individual Protein Matrix metalloproteinase-2 Homo sapiens Inhibition = 48.0 % PMID[478661]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus Inhibition = 22.0 % PMID[478661]
NPT569 Individual Protein Matrix metalloproteinase 8 Homo sapiens Inhibition = 43.0 % PMID[478661]
NPT570 Individual Protein Arachidonate 5-lipoxygenase Homo sapiens Inhibition = 81.0 % PMID[478661]
NPT43 Individual Protein Tyrosinase Agaricus bisporus Inhibition = 38.0 % PMID[478661]
NPT280 Individual Protein Matrix metalloproteinase 9 Homo sapiens Inhibition = 45.0 % PMID[478661]
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Inhibition = 29.0 % PMID[478661]
NPT1346 Individual Protein Polymerase acidic protein Influenza A virus (A/Puerto Rico/8/1934(H1N1)) IC50 = 22500.0 nM PMID[478663]
NPT1346 Individual Protein Polymerase acidic protein Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Inhibition > 80.0 % PMID[478663]
NPT1346 Individual Protein Polymerase acidic protein Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Inhibition > 50.0 % PMID[478663]
NPT1346 Individual Protein Polymerase acidic protein Influenza A virus (A/Puerto Rico/8/1934(H1N1)) IC50 = 25118.86 nM PMID[478663]
NPT35 Others n.a. pKa2 = 8.7 n.a. PMID[478659]
NPT35 Others n.a. Log beta3 = 28.4 n.a. PMID[478659]
NPT27 Others Unspecified mean log D = -0.92 n.a. PMID[478660]
NPT27 Others Unspecified mean log D = -2.0 n.a. PMID[478660]
NPT27 Others Unspecified mean log D = -1.48 n.a. PMID[478660]
NPT27 Others Unspecified mean log D = -1.18 n.a. PMID[478660]
NPT69 Individual Protein Matrix metalloproteinase-1 Homo sapiens Inhibition = 48.0 % PMID[478661]
NPT2 Others Unspecified IC50 = 22500.0 nM PMID[478662]
NPT2 Others Unspecified IC50 = 25118.86 nM PMID[478662]

☑ 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 NPC2741 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
0.881 High Similarity NPC158853
0.72 Intermediate Similarity NPC116366
0.6596 Remote Similarity NPC75134
0.6596 Remote Similarity NPC106547
0.6458 Remote Similarity NPC110396
0.6415 Remote Similarity NPC135537
0.6078 Remote Similarity NPC313553
0.6053 Remote Similarity NPC94980
0.5962 Remote Similarity NPC220191
0.5962 Remote Similarity NPC107703
0.5952 Remote Similarity NPC304788
0.5893 Remote Similarity NPC51846
0.5849 Remote Similarity NPC22329
0.5741 Remote Similarity NPC46565
0.5741 Remote Similarity NPC229046
0.5741 Remote Similarity NPC137396
0.5636 Remote Similarity NPC168521
0.5636 Remote Similarity NPC474805
0.561 Remote Similarity NPC155900

  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 NPC2741 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
0.881 High Similarity NPD9090 Phase 3
0.8095 Intermediate Similarity NPD9297 Discontinued
0.8095 Intermediate Similarity NPD9091 Suspended
0.569 Remote Similarity NPD9306 Approved
0.5614 Remote Similarity NPD9286 Clinical (unspecified phase)

  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