Structure

Physi-Chem Properties

Molecular Weight:  272.07
Volume:  267.823
LogP:  2.538
LogD:  2.127
LogS:  -3.327
# Rotatable Bonds:  1
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.694
Synthetic Accessibility Score:  2.831
Fsp3:  0.133
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.27
MDCK Permeability:  1.0296487744199112e-05
Pgp-inhibitor:  0.084
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.742
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.036
Plasma Protein Binding (PPB):  97.73172760009766%
Volume Distribution (VD):  0.437
Pgp-substrate:  2.3986637592315674%

ADMET: Metabolism

CYP1A2-inhibitor:  0.667
CYP1A2-substrate:  0.132
CYP2C19-inhibitor:  0.362
CYP2C19-substrate:  0.072
CYP2C9-inhibitor:  0.812
CYP2C9-substrate:  0.798
CYP2D6-inhibitor:  0.666
CYP2D6-substrate:  0.32
CYP3A4-inhibitor:  0.31
CYP3A4-substrate:  0.178

ADMET: Excretion

Clearance (CL):  14.86
Half-life (T1/2):  0.824

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.114
Drug-inuced Liver Injury (DILI):  0.955
AMES Toxicity:  0.229
Rat Oral Acute Toxicity:  0.678
Maximum Recommended Daily Dose:  0.04
Skin Sensitization:  0.934
Carcinogencity:  0.581
Eye Corrosion:  0.004
Eye Irritation:  0.921
Respiratory Toxicity:  0.337

Download Data

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

  Natural Product: NPC169454

Natural Product ID:  NPC169454
Common Name*:   GPDJGLOROGNHJD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GPDJGLOROGNHJD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H12O5/c16-9-6-11(8-4-2-1-3-5-8)20-12-7-10(17)14(18)15(19)13(9)12/h1-5,7,11,17-19H,6H2
SMILES:  c1ccc(cc1)C1CC(=O)c2c(cc(c(c2O)O)O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   9816931
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

*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
NPO21324 Plantago major Species Plantaginaceae Eukaryota Whole Plant the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Entire plants the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19829679]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[19948405]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. root n.a. PMID[21087019]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22314230]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23521110]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. seed n.a. PMID[23672042]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[2488968]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[24895551]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[2610694]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[9784154]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9834167]
NPO18655 Clerodendranthus spicatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25459 Scutellaria rehderiana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28574 Oroxylum indicum Species Bignoniaceae 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]
NPO21524 Scutellaria hypericifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13167 Scutellaria amoena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5431 Scutellaria likiangensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25459 Scutellaria rehderiana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5431 Scutellaria likiangensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18655 Clerodendranthus spicatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18030 Herba acalyphae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO21524 Scutellaria hypericifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28574 Oroxylum indicum Species Bignoniaceae 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]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13167 Scutellaria amoena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21524 Scutellaria hypericifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13167 Scutellaria amoena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5431 Scutellaria likiangensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25459 Scutellaria rehderiana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5431 Scutellaria likiangensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25459 Scutellaria rehderiana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13167 Scutellaria amoena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21524 Scutellaria hypericifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18655 Clerodendranthus spicatus Species Lamiaceae 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 NPC169454 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 NPC169454 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