Structure

Physi-Chem Properties

Molecular Weight:  348.19
Volume:  362.212
LogP:  2.906
LogD:  2.831
LogS:  -3.596
# Rotatable Bonds:  1
TPSA:  68.29
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.194
Synthetic Accessibility Score:  5.272
Fsp3:  0.65
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  3
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.65
MDCK Permeability:  4.598172381520271e-05
Pgp-inhibitor:  0.214
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.048
20% Bioavailability (F20%):  0.026
30% Bioavailability (F30%):  0.623

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.182
Plasma Protein Binding (PPB):  81.22428131103516%
Volume Distribution (VD):  0.888
Pgp-substrate:  10.41562557220459%

ADMET: Metabolism

CYP1A2-inhibitor:  0.038
CYP1A2-substrate:  0.094
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.379
CYP2C9-inhibitor:  0.088
CYP2C9-substrate:  0.111
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.514
CYP3A4-inhibitor:  0.317
CYP3A4-substrate:  0.266

ADMET: Excretion

Clearance (CL):  10.006
Half-life (T1/2):  0.133

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.627
Drug-inuced Liver Injury (DILI):  0.485
AMES Toxicity:  0.832
Rat Oral Acute Toxicity:  0.573
Maximum Recommended Daily Dose:  0.914
Skin Sensitization:  0.917
Carcinogencity:  0.838
Eye Corrosion:  0.637
Eye Irritation:  0.358
Respiratory Toxicity:  0.974

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  Natural Product: NPC3658

Natural Product ID:  NPC3658
Common Name*:   CSKUUHDAPAWYTK-NNEDUNNPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CSKUUHDAPAWYTK-NNEDUNNPSA-N
Standard InCHI:  InChI=1S/C20H28O5/c1-12-6-5-7-13(2)16(25-22)8-9-20(4)18(24-20)11-15-14(3)19(21)23-17(15)10-12/h6,15-18,22H,2-3,5,7-11H2,1,4H3/b12-6+/t15-,16+,17+,18+,20+/m1/s1
SMILES:  C/C/1=CCCC(=C)[C@H](CC[C@@]2(C)[C@H](C[C@@H]3C(=C)C(=O)O[C@H]3C1)O2)OO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO25715 Senna siamea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10757709]
NPO9909 Sarcophyton crassocaule Species Alcyoniidae Eukaryota n.a. formosan soft coral n.a. PMID[11141104]
NPO15773 Ecteinascidia thurstoni Species Perophoridae Eukaryota n.a. Thai n.a. PMID[12088444]
NPO10443 Sloanea zuliaensis Species Elaeocarpaceae Eukaryota n.a. n.a. n.a. PMID[14640532]
NPO16560 Palhinhaea cernua Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[16872152]
NPO9909 Sarcophyton crassocaule Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[17067165]
NPO9909 Sarcophyton crassocaule Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[17125220]
NPO25715 Senna siamea Species Fabaceae Eukaryota n.a. leaf n.a. PMID[17685627]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO9909 Sarcophyton crassocaule Species Alcyoniidae Eukaryota n.a. Formosan soft coral n.a. PMID[22014827]
NPO25715 Senna siamea Species Fabaceae Eukaryota Stems n.a. n.a. PMID[23078294]
NPO25715 Senna siamea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23513740]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO16560 Palhinhaea cernua Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[31994397]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO16101 Gleditsia triacanthos Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13417 Campanula medium Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13931 Selaginella uncinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20404.1 Eruca vesicaria subsp. sativa Subspecies Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO13417 Campanula medium Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13931 Selaginella uncinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16101 Gleditsia triacanthos Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13577 Pieris formosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16560 Palhinhaea cernua Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20404.1 Eruca vesicaria subsp. sativa Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25715 Senna siamea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14909 Artemisia caerulescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16453 Lycium cestroides Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15037 Echinops spinosissimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6809 Cailliea cinerea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26988 Acinos thymoides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10443 Sloanea zuliaensis Species Elaeocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11762 Agrimonia eupatoria Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13733 Saccharopolyspora erythraea Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9909 Sarcophyton crassocaule Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16534 Pterocaulon alopecuroides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26508 Uvariopsis tripetala Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5719 Hedyotis lawsoniae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13417 Campanula medium Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13931 Selaginella uncinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15428 Cheilanthes tenuifolia Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15983 Udotea cyathiformis Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11365 Lecidea lithophila Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16617 Paepalanthus hilairei Species Eriocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12764 Tillandsia fragrans Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15879 Euphorbia nivulia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16101 Gleditsia triacanthos Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO73 Pseudanabaena persicina Species Pseudanabaenaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12451 Dermocybe cinnabarina Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12217 Buccinum undatum Species Buccinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16774 Hermidium alipes n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14434 Alluaudia humbertii Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13577 Pieris formosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16560 Palhinhaea cernua Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14591 Rhabdodendron amazonicum Species Rhabdodendraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16301 Ilex macropoda Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2584 Monostroma fuscum Species Monostromataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16740 Helipterum venustum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25715 Senna siamea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25278 Cystofilobasidium infirmominiatum Species Cystofilobasidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10877 Humboldtia laurifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1655 Corydendrium parasiticum Species Oceaniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15674 Acanthosyris spinescens Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5127 Cladocroce incurvata Species Chalinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13264 Alstonia lanceolifera Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9314 Gouania ulmifolia Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7023 Tetracera rosiflora Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15773 Ecteinascidia thurstoni Species Perophoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16206 Umbilicaria indica Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13036 Culicinomyces clavisporus Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20404.1 Eruca vesicaria subsp. sativa Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO639 Formica polyctena Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14107 Teucrium montanum Species Lamiaceae 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 NPC3658 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 NPC3658 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