Structure

Physi-Chem Properties

Molecular Weight:  270.09
Volume:  270.409
LogP:  3.82
LogD:  3.529
LogS:  -6.217
# Rotatable Bonds:  0
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.677
Synthetic Accessibility Score:  2.954
Fsp3:  0.375
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.828
MDCK Permeability:  3.350806582602672e-05
Pgp-inhibitor:  0.775
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.979
30% Bioavailability (F30%):  0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.018
Plasma Protein Binding (PPB):  89.76209259033203%
Volume Distribution (VD):  2.148
Pgp-substrate:  3.1117780208587646%

ADMET: Metabolism

CYP1A2-inhibitor:  0.989
CYP1A2-substrate:  0.283
CYP2C19-inhibitor:  0.963
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.845
CYP2C9-substrate:  0.831
CYP2D6-inhibitor:  0.933
CYP2D6-substrate:  0.234
CYP3A4-inhibitor:  0.662
CYP3A4-substrate:  0.143

ADMET: Excretion

Clearance (CL):  10.483
Half-life (T1/2):  0.284

ADMET: Toxicity

hERG Blockers:  0.113
Human Hepatotoxicity (H-HT):  0.062
Drug-inuced Liver Injury (DILI):  0.244
AMES Toxicity:  0.086
Rat Oral Acute Toxicity:  0.528
Maximum Recommended Daily Dose:  0.883
Skin Sensitization:  0.777
Carcinogencity:  0.525
Eye Corrosion:  0.003
Eye Irritation:  0.139
Respiratory Toxicity:  0.021

Download Data

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

  Natural Product: NPC78617

Natural Product ID:  NPC78617
Common Name*:   CACOEDMTMUFXDB-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CACOEDMTMUFXDB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H14O4/c17-15-12-2-1-9-7-10-3-5-19-16(18)14(10)8-13(9)11(12)4-6-20-15/h7-8H,1-6H2
SMILES:  C1CC2=C(CCOC2=O)c2cc3c(CCOC3=O)cc12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   46209730
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001640] Naphthopyrans
        • [CHEMONTID:0001641] Naphthopyranones

*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
NPO25228 Corollospora pulchella Species Halosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[9666182]
NPO24661 Leontice leontopetalum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23292 Andrographis macrobotrys Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24661 Leontice leontopetalum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21804 Dryopteris villarii Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25228 Corollospora pulchella Species Halosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24875 Lithocarpus litseifolius Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25134 Cephalosporium chrysogenum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23166 Keteleeria evelyniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25070 Naranga aenescens n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22424 Cetraria ornata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13483 Silene praemixta Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19759 Begonia fagifolia Species Begoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22085 Cercospora traversiana Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11200.1 Paenibacillus larvae subsp. pulvifaciens Subspecies Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24468 Zanthoxylum macrophyllum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2825 Chiloscyphus pallescens Species Lophocoleaceae 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 NPC78617 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 NPC78617 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