Structure

Physi-Chem Properties

Molecular Weight:  184.07
Volume:  176.995
LogP:  1.098
LogD:  1.047
LogS:  -1.829
# Rotatable Bonds:  1
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.443
Synthetic Accessibility Score:  4.325
Fsp3:  0.667
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:  -4.693
MDCK Permeability:  0.00012875245010945946
Pgp-inhibitor:  0.004
Pgp-substrate:  0.028
Human Intestinal Absorption (HIA):  0.079
20% Bioavailability (F20%):  0.92
30% Bioavailability (F30%):  0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.99
Plasma Protein Binding (PPB):  48.74940490722656%
Volume Distribution (VD):  1.005
Pgp-substrate:  58.74344253540039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.324
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.109
CYP3A4-inhibitor:  0.033
CYP3A4-substrate:  0.243

ADMET: Excretion

Clearance (CL):  5.854
Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.143
Drug-inuced Liver Injury (DILI):  0.549
AMES Toxicity:  0.043
Rat Oral Acute Toxicity:  0.347
Maximum Recommended Daily Dose:  0.779
Skin Sensitization:  0.221
Carcinogencity:  0.894
Eye Corrosion:  0.01
Eye Irritation:  0.545
Respiratory Toxicity:  0.071

Download Data

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

  Natural Product: NPC176471

Natural Product ID:  NPC176471
Common Name*:   QTCDAEXXECYNNS-MUWHJKNJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QTCDAEXXECYNNS-MUWHJKNJSA-N
Standard InCHI:  InChI=1S/C9H12O4/c10-5-9(12)7-3-1-2-6(7)4-8(11)13-9/h3,6,10,12H,1-2,4-5H2/t6-,9+/m1/s1
SMILES:  C1C[C@@H]2CC(=O)O[C@@](CO)(C2=C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001244] Delta valerolactones

*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
NPO17605 Adenaria floribunda Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[15043429]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22209460]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24253739]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28860 Saprosma scortechinii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28860 Saprosma scortechinii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29448 Centaurea thessala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12447 Plagiochila yokogurensis Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29077 Marsupella emarginata Species Gymnomitriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29197 Mimosa hostilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29342 Astraeus hygrometricus Species Astraeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22440 Arctanthemum arcticum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28914 Caragana sinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29186 Nardosmia laevigata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28580 Tetragonia tetragonioides Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29122 Scyphiphora hydrophyllacea Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29291 Diplopappus fruticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17605 Adenaria floribunda Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29527 Stemonoporus affinis Species Dipterocarpaceae 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

☑ 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 NPC176471 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

  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 NPC176471 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

  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