Structure

Physi-Chem Properties

Molecular Weight:  152.08
Volume:  165.335
LogP:  2.683
LogD:  2.936
LogS:  -2.864
# Rotatable Bonds:  2
TPSA:  18.46
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.645
Synthetic Accessibility Score:  1.48
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:  -4.454
MDCK Permeability:  2.186580968555063e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.34
30% Bioavailability (F30%):  0.816

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.888
Plasma Protein Binding (PPB):  90.65726470947266%
Volume Distribution (VD):  1.476
Pgp-substrate:  6.454808235168457%

ADMET: Metabolism

CYP1A2-inhibitor:  0.956
CYP1A2-substrate:  0.95
CYP2C19-inhibitor:  0.769
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.1
CYP2C9-substrate:  0.885
CYP2D6-inhibitor:  0.623
CYP2D6-substrate:  0.931
CYP3A4-inhibitor:  0.303
CYP3A4-substrate:  0.433

ADMET: Excretion

Clearance (CL):  11.186
Half-life (T1/2):  0.762

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.186
Drug-inuced Liver Injury (DILI):  0.339
AMES Toxicity:  0.083
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.077
Skin Sensitization:  0.845
Carcinogencity:  0.115
Eye Corrosion:  0.973
Eye Irritation:  0.991
Respiratory Toxicity:  0.162

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  Natural Product: NPC186903

Natural Product ID:  NPC186903
Common Name*:   RIZBLVRXRWHLFA-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RIZBLVRXRWHLFA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H12O2/c1-7-4-8(10-2)6-9(5-7)11-3/h4-6H,1-3H3
SMILES:  Cc1cc(cc(c1)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   77844
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0004113] Methoxybenzenes
          • [CHEMONTID:0004111] Dimethoxybenzenes

*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
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. root n.a. DOI[10.1007/s11418-007-0221-0]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[12502328]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. PMID[15387676]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[17157006]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[19217780]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[21070010]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. aerial part n.a. PMID[21070010]
NPO16877 Aconitum episcopale Species Ranunculaceae Eukaryota n.a. root n.a. PMID[21417277]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[21953622]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[22365754]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[27329938]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota Twigs n.a. n.a. PMID[32520551]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[33296199]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[3373224]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[7775984]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae 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]
NPO13989 Uncaria macrophylla Species Rubiaceae 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]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae 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]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6336 Asarum sieboldii Species Aristolochiaceae 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]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota 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]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13926 Protaetia cuprea Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10906 Pinus koraiensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3741 Pagrus major Species Sparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15193 Cacia concinna n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO745 Rubus trifidus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16877 Aconitum episcopale Species Ranunculaceae 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]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13989 Uncaria macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16552 Aromia moschata Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9962 Pocillopora damicornis Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7909 Parmelia vittata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16119 Eucalyptus hybrid Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11421 Arnebia euchroma Species Boraginaceae 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]
NPO15462 Angelica sinensis Species Apiaceae 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 NPC186903 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 NPC186903 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