Structure

Physi-Chem Properties

Molecular Weight:  205.06
Volume:  198.456
LogP:  1.271
LogD:  0.278
LogS:  -1.168
# Rotatable Bonds:  7
TPSA:  35.42
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.276
Synthetic Accessibility Score:  4.463
Fsp3:  0.875
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.548
MDCK Permeability:  4.5343062083702534e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.619
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.4
Plasma Protein Binding (PPB):  18.456836700439453%
Volume Distribution (VD):  1.249
Pgp-substrate:  81.66287994384766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.059
CYP1A2-substrate:  0.571
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.789
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.106
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.353
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.2

ADMET: Excretion

Clearance (CL):  6.783
Half-life (T1/2):  0.792

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.257
Drug-inuced Liver Injury (DILI):  0.579
AMES Toxicity:  0.687
Rat Oral Acute Toxicity:  0.776
Maximum Recommended Daily Dose:  0.33
Skin Sensitization:  0.811
Carcinogencity:  0.746
Eye Corrosion:  0.957
Eye Irritation:  0.979
Respiratory Toxicity:  0.974

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

  Natural Product: NPC149602

Natural Product ID:  NPC149602
Common Name*:   XQZVZULJKVALRI-LBPRGKRZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XQZVZULJKVALRI-LBPRGKRZSA-N
Standard InCHI:  InChI=1S/C8H15NOS2/c1-12(10)7-5-3-2-4-6-9-8-11/h2-7H2,1H3/t12-/m0/s1
SMILES:  C[S@](=O)CCCCCCN=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3337756
PubChem CID:   NA
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0000491] Sulfoxides

*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
NPO28141 Colpomenia sinuosa Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50097a033]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[12802735]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[18384095]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[22014120]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[22014120]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[22014168]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. root n.a. PMID[22779710]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[22779710]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[23540838]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[24295708]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[25102361]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[25306330]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[31625742]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15118 Paederia chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO15118 Paederia chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16314 Clematis terniflora Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28646 Streptomyces argenteolus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11079 Centaurea regia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28195 Phlogacanthus tubiflorus Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13725 Kallstroemia pubescens Species Zygophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28141 Colpomenia sinuosa Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27829 Aplophyllum pedicellatum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27905 Eritrichium sericeum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28556 Streptomyces pentaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19765 Melampyrum nemorosum Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15118 Paederia chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28263 Anemone tomentosa Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28070 Chrysosplenium americanum Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16314 Clematis terniflora Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21557 Woodsia manchuriensis Species Woodsiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20714 Lobophytum schoedei Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17111 Myriactis humilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23326 Bohadschia vitiensis Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28422 Sabia japonica Species Sabiaceae 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
NPT171 Cell Line MRC5 Homo sapiens GI = 20.0 % PMID[560279]
NPT81 Cell Line A549 Homo sapiens GI = 50.0 % PMID[560279]
NPT171 Cell Line MRC5 Homo sapiens IC50 = 17580.0 nM PMID[560279]
NPT81 Cell Line A549 Homo sapiens IC50 = 7540.0 nM PMID[560279]

☑ 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 NPC149602 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
0.9444 High Similarity NPC140734
0.8889 High Similarity NPC171713
0.8889 High Similarity NPC105023
0.8889 High Similarity NPC266113
0.8889 High Similarity NPC292366
0.8421 Intermediate Similarity NPC180872
0.8421 Intermediate Similarity NPC235767
0.75 Intermediate Similarity NPC172064
0.6389 Remote Similarity NPC106203
0.6364 Remote Similarity NPC205586
0.5833 Remote Similarity NPC245814

  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 NPC149602 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
0.6 Remote Similarity NPD629 Approved

  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