Structure

Physi-Chem Properties

Molecular Weight:  302.1
Volume:  278.704
LogP:  -0.712
LogD:  -0.575
LogS:  -0.591
# Rotatable Bonds:  4
TPSA:  128.84
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.458
Synthetic Accessibility Score:  3.419
Fsp3:  0.538
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:  -6.06
MDCK Permeability:  5.1524886657716706e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.131
Human Intestinal Absorption (HIA):  0.551
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.883

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.306
Plasma Protein Binding (PPB):  32.30329132080078%
Volume Distribution (VD):  0.623
Pgp-substrate:  52.91148376464844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.061
CYP1A2-substrate:  0.115
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.614
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.576
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.455
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  2.983
Half-life (T1/2):  0.898

ADMET: Toxicity

hERG Blockers:  0.137
Human Hepatotoxicity (H-HT):  0.043
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.251
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.406
Carcinogencity:  0.097
Eye Corrosion:  0.01
Eye Irritation:  0.186
Respiratory Toxicity:  0.03

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  Natural Product: NPC138287

Natural Product ID:  NPC138287
Common Name*:   LWEHRPZXRYZMDC-UJPOAAIJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LWEHRPZXRYZMDC-UJPOAAIJSA-N
Standard InCHI:  InChI=1S/C13H18O8/c1-19-8-4-6(15)2-3-7(8)20-13-12(18)11(17)10(16)9(5-14)21-13/h2-4,9-18H,5H2,1H3/t9-,10-,11+,12-,13-/m1/s1
SMILES:  COc1cc(ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15098566
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
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[11032480]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. bark n.a. PMID[21192716]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. PMID[22466953]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. PMID[24450804]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO277 Caulis millettiae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25479 Sabal blackburniana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22798 Pseudofumaria lutea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22798 Pseudofumaria lutea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12213 Perriera orientalis Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5383 Othonna dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5932 Berchemia racemosa Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6297 Cinchona tucujensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6938 Astragalus dissectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8181 Hypoxylon tinctor Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2384 Ircinia ramosa Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12021 Artemisia incanescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13600 Ichthyothere latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10325 Boletus pini Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3075 Dimorphotheca aurantiaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7758 Streptomyces caespitosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6599 Neorautanenia ficifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29152 Caloboletus calopus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9620 Rhodococcus fascians Species 0cardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25479 Sabal blackburniana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13790 Abedus herberti Species Belostomatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26723 Lachnophyllum gossypinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14078 Paramecium tetraurelia Species Parameciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9017 Fagus grandifolia Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13685 Scrophularia umbrosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7705 Navanax inermis Species Aglajidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8628 Strychnos erichsonii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12716 Stocksia brahuica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12564 Sinularia facile Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13987 Solanum sublobatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8186 Ocotea minarum Species Lauraceae 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 NPC138287 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 NPC138287 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