Structure

Physi-Chem Properties

Molecular Weight:  208.07
Volume:  212.234
LogP:  2.07
LogD:  2.389
LogS:  -2.423
# Rotatable Bonds:  4
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.766
Synthetic Accessibility Score:  1.687
Fsp3:  0.182
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:  -4.682
MDCK Permeability:  1.4721936167916283e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.067
Human Intestinal Absorption (HIA):  0.051
20% Bioavailability (F20%):  0.115
30% Bioavailability (F30%):  0.578

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.697
Plasma Protein Binding (PPB):  84.8405532836914%
Volume Distribution (VD):  0.392
Pgp-substrate:  9.399200439453125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.075
CYP1A2-substrate:  0.839
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.103
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.517
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.289
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  7.717
Half-life (T1/2):  0.918

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.395
Drug-inuced Liver Injury (DILI):  0.651
AMES Toxicity:  0.044
Rat Oral Acute Toxicity:  0.142
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.946
Carcinogencity:  0.479
Eye Corrosion:  0.229
Eye Irritation:  0.937
Respiratory Toxicity:  0.793

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

  Natural Product: NPC279459

Natural Product ID:  NPC279459
Common Name*:   HJBWJAPEBGSQPR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HJBWJAPEBGSQPR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H12O4/c1-14-9-5-3-8(4-6-11(12)13)7-10(9)15-2/h3-7H,1-2H3,(H,12,13)
SMILES:  COc1ccc(C=CC(=O)O)cc1OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16848
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives
          • [CHEMONTID:0000059] Coumaric 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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11551759]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. whole plant n.a. PMID[21214467]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15215 Hypericum androsaemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15215 Hypericum androsaemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO292 Aglaia elliptica Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3999 Salix acutifolia Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17074 Trichosurus vulpecula Species Phalangeridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6134 Vitis betulifolia Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1906 Catananche caerulea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10898 Diospyros morrisiana Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5424 Phebalium whitei Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3758 Stiretrus anchorago Species Pentatomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5266 Strychnos ligustrina Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14424 Planococcus citri Species Pseudococcidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7912 Salvia urolepis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO718 Corydalis calliantha Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5984 Rosa agrestis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15263 Myrciaria dubia Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4566 Solanderia secunda Species Hydractiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4295 Agarum cribrosum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14301 Mucor globosus Species Mucoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2570 Cirsium wallichii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2426 Corynascus setosus Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4819 Dryocosmus kuriphilus Species Cynipidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7469 Veronica kellereri Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15215 Hypericum androsaemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO292 Aglaia elliptica Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3978 Exochomus quadripustulatus Species Coccinellidae 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 NPC279459 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 NPC279459 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