Structure

Physi-Chem Properties

Molecular Weight:  259.08
Volume:  255.37
LogP:  2.045
LogD:  2.251
LogS:  -3.71
# Rotatable Bonds:  2
TPSA:  53.6
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.708
Synthetic Accessibility Score:  2.634
Fsp3:  0.214
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:  -4.737
MDCK Permeability:  3.909121369360946e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.111
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.877
Plasma Protein Binding (PPB):  81.82109832763672%
Volume Distribution (VD):  0.584
Pgp-substrate:  11.696325302124023%

ADMET: Metabolism

CYP1A2-inhibitor:  0.946
CYP1A2-substrate:  0.966
CYP2C19-inhibitor:  0.797
CYP2C19-substrate:  0.82
CYP2C9-inhibitor:  0.431
CYP2C9-substrate:  0.877
CYP2D6-inhibitor:  0.146
CYP2D6-substrate:  0.88
CYP3A4-inhibitor:  0.28
CYP3A4-substrate:  0.523

ADMET: Excretion

Clearance (CL):  5.191
Half-life (T1/2):  0.418

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.216
Drug-inuced Liver Injury (DILI):  0.862
AMES Toxicity:  0.784
Rat Oral Acute Toxicity:  0.756
Maximum Recommended Daily Dose:  0.169
Skin Sensitization:  0.1
Carcinogencity:  0.893
Eye Corrosion:  0.005
Eye Irritation:  0.387
Respiratory Toxicity:  0.925

Download Data

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

  Natural Product: NPC5092

Natural Product ID:  NPC5092
Common Name*:   LPUGGFROWXFRHP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LPUGGFROWXFRHP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H13NO4/c1-15-11-8(4-5-10(17-2)13(11)18-3)12(16)9-6-7-19-14(9)15/h4-7H,1-3H3
SMILES:  Cn1c2c(ccc(c2OC)OC)c(=O)c2ccoc12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   621199
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines and derivatives
        • [CHEMONTID:0002374] Furanoquinolines

*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
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[20943395]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[3236012]
NPO81 Erythrina orientalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3215 Phora atra Species Phoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9318 Stevia serrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO924 Russula subnigricans Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28383 Vernonia tufnellae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11244 Chrysolaena propinqua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12990 Umbelopsis vinacea Species Umbelopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8378 Fagara heitzii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6557 Lotus villosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5060 Onychopetalum amazonicum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9469 Digitalis obscura Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25530 Daphne blagayana Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29440 Sarcomyxa serotina Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4442 Artemisia austriaca Species Asteraceae 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 NPC5092 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 NPC5092 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