Structure

Physi-Chem Properties

Molecular Weight:  192.08
Volume:  197.524
LogP:  2.121
LogD:  1.837
LogS:  -2.077
# Rotatable Bonds:  1
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.467
Synthetic Accessibility Score:  4.483
Fsp3:  0.364
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:  -4.595
MDCK Permeability:  1.6939326087594964e-05
Pgp-inhibitor:  0.015
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.984
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.739
Plasma Protein Binding (PPB):  73.20059204101562%
Volume Distribution (VD):  1.866
Pgp-substrate:  23.601505279541016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.885
CYP1A2-substrate:  0.501
CYP2C19-inhibitor:  0.378
CYP2C19-substrate:  0.372
CYP2C9-inhibitor:  0.15
CYP2C9-substrate:  0.158
CYP2D6-inhibitor:  0.523
CYP2D6-substrate:  0.334
CYP3A4-inhibitor:  0.659
CYP3A4-substrate:  0.37

ADMET: Excretion

Clearance (CL):  4.412
Half-life (T1/2):  0.645

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.721
Drug-inuced Liver Injury (DILI):  0.047
AMES Toxicity:  0.7
Rat Oral Acute Toxicity:  0.31
Maximum Recommended Daily Dose:  0.878
Skin Sensitization:  0.498
Carcinogencity:  0.965
Eye Corrosion:  0.003
Eye Irritation:  0.06
Respiratory Toxicity:  0.55

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

  Natural Product: NPC315566

Natural Product ID:  NPC315566
Common Name*:   ZCODMIYKDUJOKK-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZCODMIYKDUJOKK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H12O3/c1-3-8-7(2)14-6-10-9(8)4-5-13-11(10)12/h3-4,6-8H,1,5H2,2H3
SMILES:  CC1C(C2=CCOC(=O)C2=CO1)C=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   53399182
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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
NPO23023 Swertia pubescens Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO14535 Swertia fasciculata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(89)80400-5]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.bse.2004.02.008]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. whole plant n.a. DOI[10.1021/jo00025a032]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50072a022]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[10705751]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. seed n.a. PMID[12822897]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. root n.a. PMID[16335823]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota roots n.a. n.a. PMID[17375953]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. rhizome n.a. PMID[17404979]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[18064621]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18064621]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[20677781]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[20813533]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. root n.a. PMID[22233034]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[2239318]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[23599008]
NPO9824 Swertia kouitchensis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[23805995]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[24257774]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. root n.a. PMID[26129938]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[33052051]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4472648]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[7513747]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[7561895]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. root n.a. PMID[9397205]
NPO23835 Swertia angustifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO23835 Swertia angustifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3381 Swertia hickinii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14238.1 Swertia punicea var. lutescens Varieties Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23023 Swertia pubescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9824 Swertia kouitchensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14535 Swertia fasciculata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20836 Gentiana manshurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1111 Swertia erythrosticta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20836 Gentiana manshurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14535 Swertia fasciculata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23023 Swertia pubescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14238.1 Swertia punicea var. lutescens Varieties Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1111 Swertia erythrosticta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23835 Swertia angustifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3381 Swertia hickinii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9824 Swertia kouitchensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23984 Metagentiana rhodantha Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23835 Swertia angustifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20836 Gentiana manshurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20836 Gentiana manshurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23835 Swertia angustifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14238 Swertia punicea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14685 Swertia franchetiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20836 Gentiana manshurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10429 Gentiana scabra Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23984 Metagentiana rhodantha Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18234 Gentiana rigescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14381 Swertia pseudochinensis Species Gentianaceae 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 NPC315566 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 NPC315566 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