Structure

Physi-Chem Properties

Molecular Weight:  334.1
Volume:  319.468
LogP:  2.148
LogD:  0.94
LogS:  -2.956
# Rotatable Bonds:  5
TPSA:  86.71
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.798
Synthetic Accessibility Score:  3.2
Fsp3:  0.438
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.798
MDCK Permeability:  4.651198469218798e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.02
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  68.08904266357422%
Volume Distribution (VD):  0.185
Pgp-substrate:  48.76408386230469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.055
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.203
CYP2C9-inhibitor:  0.029
CYP2C9-substrate:  0.772
CYP2D6-inhibitor:  0.239
CYP2D6-substrate:  0.095
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.254

ADMET: Excretion

Clearance (CL):  6.206
Half-life (T1/2):  0.924

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.143
Drug-inuced Liver Injury (DILI):  0.96
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.09
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.524
Carcinogencity:  0.011
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.011

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  Natural Product: NPC48645

Natural Product ID:  NPC48645
Common Name*:   BJRNKVDFDLYUGJ-LZQZFOIKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BJRNKVDFDLYUGJ-LZQZFOIKSA-N
Standard InCHI:  InChI=1S/C12H16O7/c13-5-8-9(15)10(16)11(17)12(19-8)18-7-3-1-6(14)2-4-7/h1-4,8-17H,5H2/t8-,9-,10-,11-,12-/m1/s1
SMILES:  c1cc(ccc1O)O[C@H]1[C@@H]([C@@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   7576924
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

*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
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. whole plant n.a. PMID[16079548]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO19728 Saxifraga stolonifera Species Saxifragaceae Eukaryota n.a. n.a. n.a. PMID[17997321]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. stem n.a. PMID[21443171]
NPO6749 Bergenia crassifolia Species Saxifragaceae Eukaryota n.a. leaf n.a. PMID[24895781]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1786 Pyrus pyrifolia Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29201 Arctostaphylos uva-ursi Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2688 Pericarpium pyri n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO1786 Pyrus pyrifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6749 Bergenia crassifolia Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24916 Aristolochia debilis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13524 Pyrola japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19728 Saxifraga stolonifera Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19728 Saxifraga stolonifera Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1786 Pyrus pyrifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24916 Aristolochia debilis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29201 Arctostaphylos uva-ursi Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2688 Pericarpium pyri n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO6749 Bergenia crassifolia Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12529 Phedimus aizoon Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15601 Pyrus x bretschneideri Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13524 Pyrola japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24916 Aristolochia debilis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13524 Pyrola japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24916 Aristolochia debilis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19728 Saxifraga stolonifera Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13524 Pyrola japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14798 Origanum majorana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13524 Pyrola japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15601 Pyrus x bretschneideri Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29201 Arctostaphylos uva-ursi Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19728 Saxifraga stolonifera Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1786 Pyrus pyrifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6749 Bergenia crassifolia Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12529 Phedimus aizoon Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO366 Pyrus communis Species Rosaceae 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 NPC48645 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 NPC48645 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