Structure

Physi-Chem Properties

Molecular Weight:  234.09
Volume:  232.35
LogP:  1.806
LogD:  1.762
LogS:  -2.525
# Rotatable Bonds:  1
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.742
Synthetic Accessibility Score:  4.385
Fsp3:  0.462
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:  -4.873
MDCK Permeability:  5.4705429647583514e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.038
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.704

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.352
Plasma Protein Binding (PPB):  48.56175231933594%
Volume Distribution (VD):  1.142
Pgp-substrate:  37.002288818359375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.067
CYP1A2-substrate:  0.073
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.323
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.124
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.161
CYP3A4-inhibitor:  0.043
CYP3A4-substrate:  0.274

ADMET: Excretion

Clearance (CL):  13.118
Half-life (T1/2):  0.694

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.441
Drug-inuced Liver Injury (DILI):  0.581
AMES Toxicity:  0.75
Rat Oral Acute Toxicity:  0.159
Maximum Recommended Daily Dose:  0.801
Skin Sensitization:  0.628
Carcinogencity:  0.795
Eye Corrosion:  0.024
Eye Irritation:  0.775
Respiratory Toxicity:  0.246

Download Data

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

  Natural Product: NPC113078

Natural Product ID:  NPC113078
Common Name*:   ZPVLUTBGTWEMGV-XRRVDJEJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZPVLUTBGTWEMGV-XRRVDJEJSA-N
Standard InCHI:  InChI=1S/C13H14O4/c14-11-7-9-6-10(17-11)12(15)13(16-9)8-4-2-1-3-5-8/h1-5,9-10,12-13,15H,6-7H2/t9-,10-,12-,13+/m0/s1
SMILES:  c1ccc(cc1)[C@@H]1[C@H]([C@@H]2C[C@@H](CC(=O)O2)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11310860
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002204] C-glycosyl compounds

*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
NPO2253 Illicium jiadifengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[11975494]
NPO2558 Ceratodictyon spongiosum Species Lomentariaceae Eukaryota n.a. n.a. n.a. PMID[19670881]
NPO7761 Laurencia majuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[8691206]
NPO7761 Laurencia majuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3409 Goniothalamus leiocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1536 Lindera triloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1536 Lindera triloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2182 Athyrium filix-femina Species Athyriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7607 Ophiorrhiza pumila Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1093 Plumeria obtusa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7761 Laurencia majuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3409 Goniothalamus leiocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2253 Illicium jiadifengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3409 Goniothalamus leiocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1536 Lindera triloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7761 Laurencia majuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4276 Cupressus lindleyi Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2558 Ceratodictyon spongiosum Species Lomentariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1693 Gnomonia fragariae Species Sydowiellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4805 Balanophora papuana Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3114 Stylocheilus striatus Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1878 Kunzea baxteri Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6838 Senecio grisebachii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2253 Illicium jiadifengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2182 Athyrium filix-femina Species Athyriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1093 Plumeria obtusa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8060 Lethariella cashmeriana Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO274 Dendrobates viridis Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7607 Ophiorrhiza pumila Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2956 Echinometra oblonga Species Echinometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11725 Cetonia aurata Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3409 Goniothalamus leiocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5796 Haplopappus foliosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5262 Sargassum natans Species Sargassaceae 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 NPC113078 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 NPC113078 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