Structure

Physi-Chem Properties

Molecular Weight:  128.05
Volume:  124.874
LogP:  0.897
LogD:  1.129
LogS:  -0.687
# Rotatable Bonds:  0
TPSA:  53.6
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.553
Synthetic Accessibility Score:  2.975
Fsp3:  0.333
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:  -4.785
MDCK Permeability:  1.9717777831829153e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.048
Plasma Protein Binding (PPB):  91.00908660888672%
Volume Distribution (VD):  0.751
Pgp-substrate:  18.004596710205078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.135
CYP1A2-substrate:  0.848
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.708
CYP2C9-inhibitor:  0.031
CYP2C9-substrate:  0.696
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.591
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.313

ADMET: Excretion

Clearance (CL):  17.829
Half-life (T1/2):  0.902

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.096
Drug-inuced Liver Injury (DILI):  0.19
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.191
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.739
Carcinogencity:  0.192
Eye Corrosion:  0.902
Eye Irritation:  0.955
Respiratory Toxicity:  0.136

Download Data

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

  Natural Product: NPC107703

Natural Product ID:  NPC107703
Common Name*:   4-Hydroxy-2,5-Dimethylfuran-3-One
IUPAC Name:   4-hydroxy-2,5-dimethylfuran-3-one
Synonyms:  
Standard InCHIKey:  INAXVXBDKKUCGI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H8O3/c1-3-5(7)6(8)4(2)9-3/h3,8H,1-2H3
SMILES:  CC1C(=O)C(=C(C)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3186302
PubChem CID:   19309
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones

*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
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15670 Ananas comosus Species Bromeliaceae 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
NPO15670 NPC107703 Raw Plant 0.12 0.12 0.12 mg/100g Database [DUKE]

☑ 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 501.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 631 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 NPC107703 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
0.8913 High Similarity NPC75134
0.6949 Remote Similarity NPC187770
0.6923 Remote Similarity NPC158853
0.678 Remote Similarity NPC319423
0.6727 Remote Similarity NPC220191
0.6667 Remote Similarity NPC475618
0.6607 Remote Similarity NPC22329
0.6604 Remote Similarity NPC110396
0.6552 Remote Similarity NPC129710
0.6415 Remote Similarity NPC106547
0.6379 Remote Similarity NPC474805
0.6379 Remote Similarity NPC327103
0.6364 Remote Similarity NPC251429
0.6271 Remote Similarity NPC317796
0.623 Remote Similarity NPC474825
0.6207 Remote Similarity NPC137396
0.6176 Remote Similarity NPC94488
0.614 Remote Similarity NPC225974
0.6119 Remote Similarity NPC122627
0.6102 Remote Similarity NPC168521
0.5968 Remote Similarity NPC299369
0.5968 Remote Similarity NPC224103
0.5968 Remote Similarity NPC200831
0.5962 Remote Similarity NPC2741
0.5882 Remote Similarity NPC243272
0.5873 Remote Similarity NPC139056
0.5862 Remote Similarity NPC20934
0.5862 Remote Similarity NPC288381
0.5833 Remote Similarity NPC116366
0.5821 Remote Similarity NPC476589
0.5821 Remote Similarity NPC470123
0.5821 Remote Similarity NPC282760
0.5797 Remote Similarity NPC263382
0.5797 Remote Similarity NPC146376
0.5797 Remote Similarity NPC125578
0.5781 Remote Similarity NPC473494
0.5769 Remote Similarity NPC200147
0.5758 Remote Similarity NPC474774
0.5758 Remote Similarity NPC475073
0.5758 Remote Similarity NPC473737
0.5738 Remote Similarity NPC135537
0.5735 Remote Similarity NPC475675
0.5735 Remote Similarity NPC475555
0.5735 Remote Similarity NPC276299
0.5714 Remote Similarity NPC262673
0.5714 Remote Similarity NPC71755
0.5696 Remote Similarity NPC469884
0.5692 Remote Similarity NPC130953
0.5667 Remote Similarity NPC229046
0.5667 Remote Similarity NPC46565
0.5658 Remote Similarity NPC179933
0.5652 Remote Similarity NPC298249
0.5645 Remote Similarity NPC317548
0.5634 Remote Similarity NPC94743
0.5634 Remote Similarity NPC477455
0.5634 Remote Similarity NPC291062
0.5625 Remote Similarity NPC471223
0.5625 Remote Similarity NPC67081
0.5625 Remote Similarity NPC320421
0.5625 Remote Similarity NPC281195
0.5606 Remote Similarity NPC263732
0.5606 Remote Similarity NPC151648
0.56 Remote Similarity NPC471225
0.56 Remote Similarity NPC473536
0.56 Remote Similarity NPC272267

  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 NPC107703 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
0.6949 Remote Similarity NPD9119 Approved
0.6949 Remote Similarity NPD69 Approved
0.6923 Remote Similarity NPD9090 Phase 3
0.678 Remote Similarity NPD9118 Approved
0.6452 Remote Similarity NPD9120 Clinical (unspecified phase)
0.6346 Remote Similarity NPD9297 Discontinued
0.6346 Remote Similarity NPD9091 Suspended
0.6212 Remote Similarity NPD3704 Approved
0.5968 Remote Similarity NPD8779 Phase 3
0.5873 Remote Similarity NPD6109 Phase 1

  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