Structure

Physi-Chem Properties

Molecular Weight:  288.06
Volume:  276.613
LogP:  2.062
LogD:  1.603
LogS:  -3.479
# Rotatable Bonds:  1
TPSA:  107.22
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.599
Synthetic Accessibility Score:  2.971
Fsp3:  0.133
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.451
MDCK Permeability:  5.859755219717044e-06
Pgp-inhibitor:  0.005
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.957
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  97.39129638671875%
Volume Distribution (VD):  0.438
Pgp-substrate:  3.8527309894561768%

ADMET: Metabolism

CYP1A2-inhibitor:  0.442
CYP1A2-substrate:  0.106
CYP2C19-inhibitor:  0.274
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.785
CYP2C9-substrate:  0.809
CYP2D6-inhibitor:  0.469
CYP2D6-substrate:  0.339
CYP3A4-inhibitor:  0.349
CYP3A4-substrate:  0.162

ADMET: Excretion

Clearance (CL):  17.735
Half-life (T1/2):  0.884

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.957
AMES Toxicity:  0.313
Rat Oral Acute Toxicity:  0.633
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.947
Carcinogencity:  0.581
Eye Corrosion:  0.003
Eye Irritation:  0.924
Respiratory Toxicity:  0.168

Download Data

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

  Natural Product: NPC272753

Natural Product ID:  NPC272753
Common Name*:   FNFVAKUIMOKUQL-ZZXKWVIFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FNFVAKUIMOKUQL-ZZXKWVIFSA-N
Standard InCHI:  InChI=1S/C14H12O4/c1-9(15)3-6-11-12(17-2)7-4-10-5-8-13(16)18-14(10)11/h3-8H,1-2H3/b6-3+
SMILES:  CC(=O)/C=C/c1c(ccc2ccc(=O)oc12)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13917410
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids 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
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. whole plant n.a. PMID[16079548]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota stems n.a. n.a. PMID[19754130]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. leaf n.a. PMID[24024688]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. fruit n.a. PMID[25522543]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. PMID[7798960]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14773 Uncaria perrottetii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18677 Anagallis arvensis Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14773 Uncaria perrottetii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18677 Anagallis arvensis Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7263 Phyllobates aurotaenia Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29494 Stoeba extensa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14773 Uncaria perrottetii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7003 Streptomyces violaceochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19014 Palythoa tuberculosa Species Sphenopidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10402 Strophanthus eminii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9919 Jaspis stellifera Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9765 Petriella guttulata Species Microascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4311 Asterolasia squamuligera Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17324 Pluchea dioscoridis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11107 Stevia alpina 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 NPC272753 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 NPC272753 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