Structure

Physi-Chem Properties

Molecular Weight:  184.04
Volume:  171.773
LogP:  1.687
LogD:  1.409
LogS:  -2.138
# Rotatable Bonds:  2
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.556
Synthetic Accessibility Score:  2.178
Fsp3:  0.125
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.934
MDCK Permeability:  1.04972659755731e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.791
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.082
Plasma Protein Binding (PPB):  88.62975311279297%
Volume Distribution (VD):  0.698
Pgp-substrate:  15.313892364501953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.946
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.111
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.303
CYP2C9-substrate:  0.873
CYP2D6-inhibitor:  0.516
CYP2D6-substrate:  0.297
CYP3A4-inhibitor:  0.676
CYP3A4-substrate:  0.12

ADMET: Excretion

Clearance (CL):  15.228
Half-life (T1/2):  0.92

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.057
Drug-inuced Liver Injury (DILI):  0.754
AMES Toxicity:  0.469
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.087
Skin Sensitization:  0.76
Carcinogencity:  0.029
Eye Corrosion:  0.313
Eye Irritation:  0.941
Respiratory Toxicity:  0.282

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Similar NPs/Drugs  

  Natural Product: NPC305766

Natural Product ID:  NPC305766
Common Name*:   AQDIJIAUYXOCGX-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AQDIJIAUYXOCGX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H8O5/c1-13-8(12)7-5(10)2-4(9)3-6(7)11/h2-3,9-11H,1H3
SMILES:  COC(=O)c1c(cc(cc1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   76600
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0001248] Hydroxybenzoic acid 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
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota Whole plant n.a. n.a. PMID[11141121]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. root n.a. PMID[12612406]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota Roots n.a. n.a. PMID[32031812]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10580 Herba glechomae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6890 Euphorbia jolkinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23740 Jacobaea analoga Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18641 Radix euphorbiae pekinensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6890 Euphorbia jolkinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23740 Jacobaea analoga Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27520 Casuarina equisetifolia Species Casuarinaceae 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 NPC305766 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 NPC305766 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