Structure

Physi-Chem Properties

Molecular Weight:  354.11
Volume:  340.06
LogP:  3.644
LogD:  3.059
LogS:  -5.634
# Rotatable Bonds:  2
TPSA:  55.38
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  6
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.825
Synthetic Accessibility Score:  3.774
Fsp3:  0.4
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:  -4.966
MDCK Permeability:  5.4007290600566193e-05
Pgp-inhibitor:  0.79
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.001
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.017

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.139
Plasma Protein Binding (PPB):  96.35446166992188%
Volume Distribution (VD):  1.005
Pgp-substrate:  2.2629778385162354%

ADMET: Metabolism

CYP1A2-inhibitor:  0.771
CYP1A2-substrate:  0.234
CYP2C19-inhibitor:  0.946
CYP2C19-substrate:  0.151
CYP2C9-inhibitor:  0.778
CYP2C9-substrate:  0.802
CYP2D6-inhibitor:  0.962
CYP2D6-substrate:  0.909
CYP3A4-inhibitor:  0.968
CYP3A4-substrate:  0.334

ADMET: Excretion

Clearance (CL):  19.003
Half-life (T1/2):  0.065

ADMET: Toxicity

hERG Blockers:  0.255
Human Hepatotoxicity (H-HT):  0.203
Drug-inuced Liver Injury (DILI):  0.857
AMES Toxicity:  0.823
Rat Oral Acute Toxicity:  0.095
Maximum Recommended Daily Dose:  0.489
Skin Sensitization:  0.682
Carcinogencity:  0.886
Eye Corrosion:  0.003
Eye Irritation:  0.477
Respiratory Toxicity:  0.743

Download Data

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

  Natural Product: NPC67790

Natural Product ID:  NPC67790
Common Name*:   PEYUIKBAABKQKQ-XIDAIZRNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PEYUIKBAABKQKQ-XIDAIZRNSA-N
Standard InCHI:  InChI=1S/C20H18O6/c1-3-15-17(25-9-23-15)5-11(1)19-13-7-22-20(14(13)8-21-19)12-2-4-16-18(6-12)26-10-24-16/h1-6,13-14,19-20H,7-10H2/t13-,14-,19-,20?/m1/s1
SMILES:  c1cc2c(cc1[C@@H]1[C@@H]3COC(c4ccc5c(c4)OCO5)[C@@H]3CO1)OCO2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   233333
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans

*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
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. leaf n.a. PMID[15388977]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. stem n.a. PMID[17202689]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[17625893]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[18293924]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota Stems; Barks n.a. n.a. PMID[18303853]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota stem bark n.a. n.a. PMID[18303853]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. PMID[20192247]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. pericarp n.a. PMID[20628994]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. fruit n.a. PMID[21319773]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[22445674]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[23623680]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[25735399]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[28322565]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[28968119]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32319765]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468.2 Asarum heterotropoides f. schm. var. mandshuricum (maxim.) kitag. Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO753 Acanthopanax sessiliflorum n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9650 Zanthoxylum nitidum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. 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 NPC67790 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 NPC67790 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