Structure

Physi-Chem Properties

Molecular Weight:  112.05
Volume:  122.003
LogP:  0.481
LogD:  -0.086
LogS:  0.243
# Rotatable Bonds:  2
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.493
Synthetic Accessibility Score:  2.567
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.341
MDCK Permeability:  3.294770067441277e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.536

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.596
Plasma Protein Binding (PPB):  68.97705078125%
Volume Distribution (VD):  0.891
Pgp-substrate:  40.891563415527344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.074
CYP1A2-substrate:  0.374
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.597
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.013
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.078
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.394

ADMET: Excretion

Clearance (CL):  6.231
Half-life (T1/2):  0.909

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.373
AMES Toxicity:  0.809
Rat Oral Acute Toxicity:  0.648
Maximum Recommended Daily Dose:  0.646
Skin Sensitization:  0.867
Carcinogencity:  0.743
Eye Corrosion:  0.986
Eye Irritation:  0.991
Respiratory Toxicity:  0.967

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC180862

Natural Product ID:  NPC180862
Common Name*:   BGNXCDMCOKJUMV-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BGNXCDMCOKJUMV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H14O2/c1-10(2,3)8-6-7(11)4-5-9(8)12/h4-6,11-12H,1-3H3
SMILES:  CC(C)(C)c1cc(ccc1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16043
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0002811] Phenylpropanes

*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
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10843584]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[12713396]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[15497934]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[16441081]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16675659]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota roots n.a. n.a. PMID[20022509]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21866899]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22074222]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[22074222]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23325115]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Roots n.a. n.a. PMID[23541646]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. rhizome n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24479468]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24957203]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25445757]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25744461]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26841168]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28140583]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[28617598]
NPO40301 Prangos haussknechtii Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[28885836]
NPO40367 Streptosporangium sp. Species Streptosporangiaceae Bacteria n.a. n.a. n.a. PMID[30178674]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[30407007]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[30649869]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota Whole Fruits n.a. n.a. PMID[32159343]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32196343]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[7381508]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28734 Physalis peruviana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29384 Glycyrrhiza glabra Species Fabaceae 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 > 100000.0 nM PMID[23820128]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 5.21 n.a. PMID[24053646]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 3.24 n.a. PMID[24053646]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.06 n.a. PMID[24053646]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens EC50 = 91530.0 nM PMID[24053646]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.5 n.a. PMID[24053646]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.04 n.a. PMID[24053646]
NPT2808 Individual Protein Kelch-like ECH-associated protein 1 Homo sapiens FC = 1.12 n.a. PMID[24512214]
NPT2808 Individual Protein Kelch-like ECH-associated protein 1 Homo sapiens FC = 1.62 n.a. PMID[24512214]
NPT2808 Individual Protein Kelch-like ECH-associated protein 1 Homo sapiens FC = 2.22 n.a. PMID[24512214]
NPT2808 Individual Protein Kelch-like ECH-associated protein 1 Homo sapiens FC = 3.81 n.a. PMID[24512214]
NPT2808 Individual Protein Kelch-like ECH-associated protein 1 Homo sapiens FC = 6.21 n.a. PMID[24512214]
NPT543 Individual Protein Pregnane X receptor Homo sapiens EC50 = 12600.0 nM PMID[20966043]
NPT543 Individual Protein Pregnane X receptor Homo sapiens EC50 = 2000.0 nM PMID[20966043]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.77 n.a. PMID[25907366]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.01 n.a. PMID[26519930]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.3 n.a. PMID[26519930]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.0 n.a. PMID[26519930]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.1 n.a. PMID[26519930]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.51 n.a. PMID[26841168]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 4.34 n.a. PMID[26841168]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.18 n.a. PMID[27316545]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.25 n.a. PMID[27316545]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.24 n.a. PMID[27316545]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.14 n.a. PMID[27316545]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 5.2 n.a. PMID[27316545]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 8.46 n.a. PMID[27316545]
NPT681 Cell Line PC-12 Rattus norvegicus Activity = 0.882 % PMID[28238613]
NPT681 Cell Line PC-12 Rattus norvegicus Activity = 1.1 % PMID[28238613]
NPT681 Cell Line PC-12 Rattus norvegicus Activity = 97.1 % PMID[28238613]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 4.6 n.a. PMID[28140583]
NPT1651 Individual Protein Nuclear factor erythroid 2-related factor 2 Mus musculus CD = 1.0 uM DOI[10.1039/C6MD00456C]
NPT1651 Individual Protein Nuclear factor erythroid 2-related factor 2 Mus musculus CD = 6.0 uM DOI[10.1039/C6MD00456C]
NPT1651 Individual Protein Nuclear factor erythroid 2-related factor 2 Mus musculus Ratio = 6.0 n.a. DOI[10.1039/C6MD00456C]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 1.41 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 2.14 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 5.27 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 1.18 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 1.25 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Activity = 1.24 uM PMID[30196061]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 4.87 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 3.38 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 2.27 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.46 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.02 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.04 n.a. PMID[31283229]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.68 n.a. PMID[31859162]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.7 n.a. PMID[31859162]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 5.1 n.a. PMID[31859162]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 4.73 n.a. PMID[31859162]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens CD = 1.68 uM PMID[27736061]
NPT681 Cell Line PC-12 Rattus norvegicus Activity = 70.42 % PMID[32402936]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 82.2 % PMID[17166720]
NPT35 Others n.a. Inhibition = 90.0 % PMID[10579873]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity > 90.0 % PMID[9917288]
NPT1 Others Radical scavenging activity IC50 = 14.46 ug.mL-1 DOI[10.1007/s00044-011-9915-7]
NPT1 Others Radical scavenging activity EC50 = 36000.0 nM PMID[23711920]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. EC50 > 200000.0 nM PMID[23711920]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. EC50 = 65000.0 nM PMID[23711920]
NPT22155 PROTEIN-PROTEIN INTERACTION Keap1/Nrf2 Homo sapiens FC = 5.08 n.a. PMID[23820128]
NPT741 Individual Protein Tyrosinase Homo sapiens IC50 = 54200.0 nM PMID[25726329]
NPT35 Others n.a. EC50 = 57500.0 nM PMID[26519930]
NPT27 Others Unspecified IC50 = 147000.0 nM PMID[26970663]
NPT2 Others Unspecified CD = 1.0 uM PMID[26970663]
NPT2 Others Unspecified Ratio = 147.0 n.a. PMID[26970663]
NPT2 Others Unspecified Ratio = 6.0 n.a. PMID[26970663]
NPT2 Others Unspecified Ratio = 10.0 n.a. PMID[26970663]
NPT2 Others Unspecified CD = 6.0 uM PMID[26970663]
NPT27 Others Unspecified IC50 = 60000.0 nM PMID[26970663]
NPT2 Others Unspecified IC50 = 147000.0 nM DOI[10.1039/C6MD00456C]
NPT2 Others Unspecified Ratio = 147.0 n.a. DOI[10.1039/C6MD00456C]
NPT2 Others Unspecified IC50 = 60000.0 nM DOI[10.1039/C6MD00456C]
NPT2 Others Unspecified Ratio = 10.0 n.a. DOI[10.1039/C6MD00456C]
NPT35 Others n.a. IC50 = 150400.0 nM PMID[28885836]
NPT2 Others Unspecified IC50 = 10000.0 nM PMID[28885836]
NPT35 Others n.a. EC50 = 10000.0 nM PMID[30178674]
NPT35 Others n.a. EC50 = 482000.0 nM PMID[30178674]
NPT35 Others n.a. EC50 = 1923000.0 nM PMID[30178674]
NPT21742 CELL-LINE L02 Homo sapiens Activity <= 7.0 % PMID[30196061]
NPT2 Others Unspecified EC50 = 9900.0 nM PMID[31753804]
NPT2 Others Unspecified EC50 = 12000.0 nM PMID[31753804]
NPT2 Others Unspecified EC50 > 400000.0 nM PMID[31753804]

☑ 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 NPC180862 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 NPC180862 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