Structure

Physi-Chem Properties

Molecular Weight:  318.22
Volume:  347.268
LogP:  4.493
LogD:  3.779
LogS:  -4.783
# Rotatable Bonds:  2
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.612
Synthetic Accessibility Score:  4.849
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.488
MDCK Permeability:  2.614340883155819e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.061
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.043
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.793
Plasma Protein Binding (PPB):  70.54390716552734%
Volume Distribution (VD):  1.606
Pgp-substrate:  34.67365646362305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.08
CYP1A2-substrate:  0.406
CYP2C19-inhibitor:  0.194
CYP2C19-substrate:  0.68
CYP2C9-inhibitor:  0.245
CYP2C9-substrate:  0.155
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.353
CYP3A4-inhibitor:  0.705
CYP3A4-substrate:  0.275

ADMET: Excretion

Clearance (CL):  14.727
Half-life (T1/2):  0.03

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.11
Drug-inuced Liver Injury (DILI):  0.314
AMES Toxicity:  0.635
Rat Oral Acute Toxicity:  0.885
Maximum Recommended Daily Dose:  0.963
Skin Sensitization:  0.219
Carcinogencity:  0.472
Eye Corrosion:  0.109
Eye Irritation:  0.089
Respiratory Toxicity:  0.957

Download Data

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  Natural Product: NPC106508

Natural Product ID:  NPC106508
Common Name*:   DYYYQLXAGIXUGM-MIALQEHNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DYYYQLXAGIXUGM-MIALQEHNSA-N
Standard InCHI:  InChI=1S/C20H30O3/c1-13-6-9-16-19(2,3)10-5-11-20(16,4)15(13)8-7-14-12-17(21)23-18(14)22/h7,15-17,21H,1,5-6,8-12H2,2-4H3/t15-,16-,17+,20+/m0/s1
SMILES:  C=C1CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1CC=C1C[C@H](O)OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO26456 Jaborosa leucotricha Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[12027740]
NPO25854 Tripterospermum lanceolatum Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[1517742]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO25518 Hedychium coronarium Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[21106458]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota Leaves n.a. Database[FooDB]
NPO26113 Strychnos wallichiana Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25264 Cerbera odollam Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25962 Rhamnus cathartica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25518 Hedychium coronarium Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25264 Cerbera odollam Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25803 Strychnos elaeocarpa Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25962 Rhamnus cathartica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26610 Spiraea formosana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25518 Hedychium coronarium Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26113 Strychnos wallichiana Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25518 Hedychium coronarium Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26816 Clinopodium gracile Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25086 Viburnum betulifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26743 Lippia adoensis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26306 Pyrobaculum organotrophum Species Thermoproteaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO26079 Asterococcus muratae Species Cerococcidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24829 Gyrostroma missouriense n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24894 Parmelia tinctina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28819 Veronica liwanensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23589 Pecten irradians Species Pectinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22353 Lucilia caesar Species Calliphoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25906 Acacia linarioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26175 Spongionella gracilis Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26643 Cichorium endivia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26610 Spiraea formosana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7465 Vachellia leucophloea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13051 Perymenium jelskii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10372 Kiggelaria africana Species Achariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13072 Rhamnus formosana Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26456 Jaborosa leucotricha Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25768 Senecio ruwenzoriensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26846 Guettarda noumeana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24608 Gaertnera morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25854 Tripterospermum lanceolatum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21639 Prunus mahaleb Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26676 Daphne arisanensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17771 Senna didymobotrya Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29093 Homalium longifolium Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26208 Brombya platynema Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26357 Trachyrhamphus serratus Species Syngnathidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25732 Trichilia havanensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26481 Astragalus kabadianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14283 Ponera metallica Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24733 Celastrus dispermus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15693 Guadua angustifolia Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26392 Piptadenia colubrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25996 Stenolobium stans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23410 Potentilla candicans Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25264 Cerbera odollam Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26524 Chondria californica Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25582 Aquilegia viridiflora Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26554 Hexagonia speciosa Species Carabidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25962 Rhamnus cathartica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19916 Phenax angustifolius Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25803 Strychnos elaeocarpa Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25393 Coelogyne flavida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26113 Strychnos wallichiana Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25518 Hedychium coronarium Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25575 Streptomyces pseudovenezuelae Species Streptomycetaceae Bacteria 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 NPC106508 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 NPC106508 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