Structure

Physi-Chem Properties

Molecular Weight:  336.1
Volume:  340.473
LogP:  4.298
LogD:  3.199
LogS:  -3.496
# Rotatable Bonds:  1
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.7
Synthetic Accessibility Score:  2.84
Fsp3:  0.15
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.811
MDCK Permeability:  1.8438338884152472e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.108
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.015
Plasma Protein Binding (PPB):  99.61713409423828%
Volume Distribution (VD):  0.469
Pgp-substrate:  1.0900460481643677%

ADMET: Metabolism

CYP1A2-inhibitor:  0.967
CYP1A2-substrate:  0.387
CYP2C19-inhibitor:  0.91
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.852
CYP2C9-substrate:  0.942
CYP2D6-inhibitor:  0.948
CYP2D6-substrate:  0.781
CYP3A4-inhibitor:  0.787
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  3.759
Half-life (T1/2):  0.551

ADMET: Toxicity

hERG Blockers:  0.188
Human Hepatotoxicity (H-HT):  0.371
Drug-inuced Liver Injury (DILI):  0.439
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.421
Maximum Recommended Daily Dose:  0.907
Skin Sensitization:  0.77
Carcinogencity:  0.792
Eye Corrosion:  0.003
Eye Irritation:  0.399
Respiratory Toxicity:  0.717

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

  Natural Product: NPC107838

Natural Product ID:  NPC107838
Common Name*:   WTNXJYOYGPGIJK-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WTNXJYOYGPGIJK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H16O5/c1-20(2)6-5-12-7-11(3-4-16(12)25-20)14-10-24-17-9-13(21)8-15(22)18(17)19(14)23/h3-10,21-22H,1-2H3
SMILES:  CC1(C)C=Cc2cc(ccc2O1)c1coc2cc(cc(c2c1=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14237660
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0003530] Pyranoisoflavonoids

*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
NPO29113 Erythrina vogelii Species Fabaceae Eukaryota root bark n.a. n.a. PMID[11908991]
NPO28587 Axinella weltneri Species n.a. n.a. n.a. n.a. n.a. PMID[16124780]
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]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21123068]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. fruit n.a. PMID[21619045]
NPO13906 Ficus mucuso Species Moraceae Eukaryota figs Tongolo-Yaound, in the Central Region of Cameroon 2008-JUN PMID[21619045]
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]
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]
NPO28764 Phyllidia ocellata Species Phyllidiidae Eukaryota n.a. n.a. n.a. PMID[26056748]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26841168]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28522265]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[29641206]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32196343]
NPO28587 Axinella weltneri Species n.a. n.a. n.a. n.a. n.a. PMID[9249974]
NPO29113 Erythrina vogelii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28553 Nannoglottis ravida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1698 Glycyrrhiza inflata 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]
NPO29113 Erythrina vogelii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1698 Glycyrrhiza inflata 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]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5436 Absidia caerulea Species Cunninghamellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25617 Lactococcus lactis Species Streptococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29056 Dactynotus ambrosiae n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28517 Hypericum caprifoliatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28553 Nannoglottis ravida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28436 Helenium virginicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14750 Usnea japonica Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28587 Axinella weltneri Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28399 Anthotroche myoporoides Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28944 Heliotropium digynum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29113 Erythrina vogelii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28640 Alsidium corallinum Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28764 Phyllidia ocellata Species Phyllidiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29181 Galdieria sulphuraria Species Cyanidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28535 Astragalus flexus 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
NPT83 Cell Line MCF7 Homo sapiens GI = 2.0 % PMID[28522265]
NPT660 Cell Line SW480 Homo sapiens GI = 13.0 % PMID[28522265]
NPT65 Cell Line HepG2 Homo sapiens GI = 11.0 % PMID[28522265]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 10.0 % PMID[28522265]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens Inhibition = 27.0 % PMID[28522265]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 0.76 n.a. PMID[28835349]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens Inhibition > 60.0 % PMID[32196343]
NPT65 Cell Line HepG2 Homo sapiens Activity = 80.0 % PMID[32196343]
NPT2 Others Unspecified Inhibition = 27.0 % PMID[28522265]
NPT2 Others Unspecified Inhibition = 14.0 % PMID[28522265]
NPT2 Others Unspecified Inhibition > 40.0 % PMID[32196343]

☑ 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 NPC107838 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 NPC107838 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