Structure

Physi-Chem Properties

Molecular Weight:  260.1
Volume:  270.225
LogP:  2.308
LogD:  2.145
LogS:  -3.019
# Rotatable Bonds:  3
TPSA:  59.67
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.862
Synthetic Accessibility Score:  2.569
Fsp3:  0.267
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:  -4.638
MDCK Permeability:  1.8198596080765128e-05
Pgp-inhibitor:  0.826
Pgp-substrate:  0.14
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.173
Plasma Protein Binding (PPB):  86.74996948242188%
Volume Distribution (VD):  0.86
Pgp-substrate:  12.800630569458008%

ADMET: Metabolism

CYP1A2-inhibitor:  0.946
CYP1A2-substrate:  0.877
CYP2C19-inhibitor:  0.393
CYP2C19-substrate:  0.494
CYP2C9-inhibitor:  0.176
CYP2C9-substrate:  0.875
CYP2D6-inhibitor:  0.627
CYP2D6-substrate:  0.783
CYP3A4-inhibitor:  0.139
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  11.14
Half-life (T1/2):  0.699

ADMET: Toxicity

hERG Blockers:  0.075
Human Hepatotoxicity (H-HT):  0.594
Drug-inuced Liver Injury (DILI):  0.594
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.182
Skin Sensitization:  0.501
Carcinogencity:  0.865
Eye Corrosion:  0.023
Eye Irritation:  0.844
Respiratory Toxicity:  0.031

Download Data

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

  Natural Product: NPC168034

Natural Product ID:  NPC168034
Common Name*:   LNFVZUMSDAIQDQ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LNFVZUMSDAIQDQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H16O4/c1-15(2,17)7-6-11-8-10-4-5-14(16)19-13(10)9-12(11)18-3/h4-9,17H,1-3H3
SMILES:  CC(C)(C=Cc1cc2ccc(=O)oc2cc1OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   87695
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins 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
NPO24827 Caragana conferta Species Fabaceae Eukaryota n.a. whole plant n.a. PMID[19336940]
NPO25040 Tellina nitida Species Tellinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24870 Campanula patula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24827 Caragana conferta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24994 Thladiantha dubia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21354 Juniperus cedrus Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23770 Artemisia gmelini Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23813 Ardisia floribunda Species Primulaceae 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 NPC168034 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 NPC168034 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