Structure

Physi-Chem Properties

Molecular Weight:  168.08
Volume:  174.125
LogP:  1.688
LogD:  1.813
LogS:  -2.129
# Rotatable Bonds:  3
TPSA:  27.69
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  1.243
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.474
MDCK Permeability:  3.084710624534637e-05
Pgp-inhibitor:  0.05
Pgp-substrate:  0.028
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.28

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.909
Plasma Protein Binding (PPB):  70.56068420410156%
Volume Distribution (VD):  1.368
Pgp-substrate:  15.581857681274414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.954
CYP1A2-substrate:  0.956
CYP2C19-inhibitor:  0.711
CYP2C19-substrate:  0.907
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.873
CYP2D6-inhibitor:  0.081
CYP2D6-substrate:  0.936
CYP3A4-inhibitor:  0.139
CYP3A4-substrate:  0.453

ADMET: Excretion

Clearance (CL):  10.143
Half-life (T1/2):  0.831

ADMET: Toxicity

hERG Blockers:  0.104
Human Hepatotoxicity (H-HT):  0.145
Drug-inuced Liver Injury (DILI):  0.736
AMES Toxicity:  0.195
Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.723
Carcinogencity:  0.267
Eye Corrosion:  0.95
Eye Irritation:  0.97
Respiratory Toxicity:  0.205

Download Data

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

  Natural Product: NPC227308

Natural Product ID:  NPC227308
Common Name*:   AGIQIOSHSMJYJP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AGIQIOSHSMJYJP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H12O3/c1-10-7-4-5-8(11-2)9(6-7)12-3/h4-6H,1-3H3
SMILES:  COc1ccc(c(c1)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   67284
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002341] Phenol ethers
        • [CHEMONTID:0000138] Anisoles

*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
NPO40110 Duguetia surinamensis Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[31403289]

☑ 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
NPT233 Individual Protein Carbonic anhydrase II Homo sapiens Ki = 1430.0 nM PMID[21282059]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 10000.0 nM PMID[31403289]
NPT393 Cell Line HCT-116 Homo sapiens IC50 > 10000.0 nM PMID[31403289]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[31403289]
NPT116 Cell Line HL-60 Homo sapiens IC50 > 10000.0 nM PMID[31403289]
NPT171 Cell Line MRC5 Homo sapiens IC50 > 10000.0 nM PMID[31403289]
NPT947 Individual Protein Carbonic anhydrase I Homo sapiens Ki = 5960.0 nM PMID[21282059]
NPT948 Individual Protein Carbonic anhydrase IX Homo sapiens Ki = 4060.0 nM PMID[21282059]
NPT949 Individual Protein Carbonic anhydrase XII Homo sapiens Ki = 7800.0 nM PMID[21282059]
NPT954 Individual Protein Carbonic anhydrase XIV Homo sapiens Ki = 630.0 nM PMID[22668600]
NPT955 Individual Protein Carbonic anhydrase VII Homo sapiens Ki = 3700.0 nM PMID[22668600]

☑ 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 NPC227308 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 NPC227308 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