Structure

Physi-Chem Properties

Molecular Weight:  325.13
Volume:  324.737
LogP:  1.59
LogD:  2.777
LogS:  -2.576
# Rotatable Bonds:  1
TPSA:  51.16
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.873
Synthetic Accessibility Score:  4.116
Fsp3:  0.368
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.857
MDCK Permeability:  2.2678219465888105e-05
Pgp-inhibitor:  0.108
Pgp-substrate:  0.986
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.944

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.954
Plasma Protein Binding (PPB):  94.51689147949219%
Volume Distribution (VD):  1.093
Pgp-substrate:  4.186356544494629%

ADMET: Metabolism

CYP1A2-inhibitor:  0.88
CYP1A2-substrate:  0.938
CYP2C19-inhibitor:  0.845
CYP2C19-substrate:  0.792
CYP2C9-inhibitor:  0.15
CYP2C9-substrate:  0.612
CYP2D6-inhibitor:  0.95
CYP2D6-substrate:  0.92
CYP3A4-inhibitor:  0.923
CYP3A4-substrate:  0.919

ADMET: Excretion

Clearance (CL):  16.795
Half-life (T1/2):  0.397

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.124
Drug-inuced Liver Injury (DILI):  0.621
AMES Toxicity:  0.655
Rat Oral Acute Toxicity:  0.395
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.348
Carcinogencity:  0.857
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.884

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

  Natural Product: NPC22675

Natural Product ID:  NPC22675
Common Name*:   TZJNFQHUSMXCIT-HUUCEWRRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  TZJNFQHUSMXCIT-HUUCEWRRSA-N
Standard InCHI:  InChI=1S/C19H19NO4/c1-20-14-4-11-6-18-19(24-9-23-18)8-13(11)15(20)3-10-5-17(22-2)16(21)7-12(10)14/h5-8,14-15,21H,3-4,9H2,1-2H3/t14-,15-/m1/s1
SMILES:  CN1[C@@H]2Cc3cc4c(cc3[C@H]1Cc1cc(c(cc21)O)OC)OCO4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3082467
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002793] Pavine alkaloids

*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
NPO11277 Baeckea frutescens Species Myrtaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(98)00534-2]
NPO11277 Baeckea frutescens Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[12932146]
NPO16174 Scleropyrum wallichianum Species Cervantesiaceae Eukaryota n.a. twig n.a. PMID[16204994]
NPO1927 Isodon eriocalyx Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[17020288]
NPO15311 Cryptocarya chinensis Species Lauraceae Eukaryota leaves Lai-I, Pingtung County, Taiwan 2005-May PMID[20704331]
NPO1927 Isodon eriocalyx Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[20949916]
NPO1927 Isodon eriocalyx Species Lamiaceae Eukaryota aerial parts n.a. n.a. PMID[20949916]
NPO1927 Isodon eriocalyx Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22624550]
NPO11277 Baeckea frutescens Species Myrtaceae Eukaryota aerial parts Nanning, Guangxi Province, China 2014-OCT PMID[28753309]
NPO12301 Chenopodium quinoa Species Chenopodiaceae Eukaryota n.a. n.a. PMID[31861466]
NPO12301 Chenopodium quinoa Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15311 Cryptocarya chinensis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16174 Scleropyrum wallichianum Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15311 Cryptocarya chinensis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16174 Scleropyrum wallichianum Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13929 Hypocrella bambusae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11277 Baeckea frutescens Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11607 Marrubium parviflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15098 Cyttaria johowii Species Cyttariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15311 Cryptocarya chinensis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14344 Trifolium diffusum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7878 Lysastrosoma anthosticta n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1202 Psathyrotes ramosissima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6241 Girgensohnia oppositiflora Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14485 Eriocephalus kingesii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1927 Isodon eriocalyx Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14885 Lilium rubrum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11277 Baeckea frutescens Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14996 Lobelia syphilitica Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7036 Davidsonia pruriens Species Cunoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10936 Andira retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12818 Lespedeza maximowiczi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3521 Geranium collinum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6615 Aplidium solidum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26228 Phymatopteris hastata Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5040 Polygonatum polyanthemum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6229 Chenopodiastrum murale Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11833 Dyssodia anthemidifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12301 Chenopodium quinoa Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13040 Veretillum cynomorium Species Veretillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2770 Pyropolyporus fomentarius n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13929 Hypocrella bambusae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14086 Parthenium confertum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14223 Harpullia cupanioides Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2075 Zanthoxylum ocumarense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14366 Youngia japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12064 Lychnophora pinaster Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13241 Coprosma foetidissima Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14639 Balanophora polyandra Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20068 Fusarium striatum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15911 Streptomyces graminofaciens Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16090 Panicum crus-galli Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12296 Sphaerechinus granularis Species Toxopneustidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13755 Gonotheca helianthoides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8632 Aralia hispida Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16174 Scleropyrum wallichianum Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1946 Veronica stricta Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13631 Microglossa pyrifolia Species Asteraceae 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 NPC22675 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 NPC22675 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