Structure

Physi-Chem Properties

Molecular Weight:  284.1
Volume:  287.705
LogP:  3.509
LogD:  3.52
LogS:  -4.377
# Rotatable Bonds:  2
TPSA:  36.92
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.847
Synthetic Accessibility Score:  3.024
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.925
MDCK Permeability:  4.957050259690732e-05
Pgp-inhibitor:  0.992
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.097
Plasma Protein Binding (PPB):  97.9517593383789%
Volume Distribution (VD):  1.078
Pgp-substrate:  2.564838409423828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.687
CYP1A2-substrate:  0.963
CYP2C19-inhibitor:  0.957
CYP2C19-substrate:  0.919
CYP2C9-inhibitor:  0.869
CYP2C9-substrate:  0.912
CYP2D6-inhibitor:  0.648
CYP2D6-substrate:  0.947
CYP3A4-inhibitor:  0.832
CYP3A4-substrate:  0.865

ADMET: Excretion

Clearance (CL):  7.018
Half-life (T1/2):  0.103

ADMET: Toxicity

hERG Blockers:  0.135
Human Hepatotoxicity (H-HT):  0.171
Drug-inuced Liver Injury (DILI):  0.76
AMES Toxicity:  0.851
Rat Oral Acute Toxicity:  0.147
Maximum Recommended Daily Dose:  0.82
Skin Sensitization:  0.476
Carcinogencity:  0.489
Eye Corrosion:  0.003
Eye Irritation:  0.276
Respiratory Toxicity:  0.468

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

  Natural Product: NPC199963

Natural Product ID:  NPC199963
Common Name*:   VPGIGLKLCFOWDN-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VPGIGLKLCFOWDN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H16O4/c1-18-10-4-6-13-15(7-10)20-9-14-12-5-3-11(19-2)8-16(12)21-17(13)14/h3-8,14,17H,9H2,1-2H3
SMILES:  COc1ccc2c(c1)OCC1c3ccc(cc3OC21)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   454892
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002617] Furanoisoflavonoids
          • [CHEMONTID:0001608] Pterocarpans

*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
NPO26058 Erycibe expansa Species Convolvulaceae Eukaryota n.a. stem n.a. PMID[17077549]
NPO26058 Erycibe expansa Species Convolvulaceae Eukaryota stems n.a. n.a. PMID[17158054]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. stem n.a. PMID[19252325]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24252334]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[2488968]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[2610694]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27933899]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28960981]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26058 Erycibe expansa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9522 Pericopsis angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1209 Swartzia madagascariensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26058 Erycibe expansa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11206 Trifolium hybridum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17346 Salvia plebeia 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[TM-MC]
NPO9522 Pericopsis angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1209 Swartzia madagascariensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11206 Trifolium hybridum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1347 Maackia amurensis 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

☑ 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 NPC199963 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 NPC199963 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