Structure

Physi-Chem Properties

Molecular Weight:  348.19
Volume:  356.292
LogP:  2.639
LogD:  1.528
LogS:  -4.177
# Rotatable Bonds:  1
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.499
Synthetic Accessibility Score:  6.028
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.854
MDCK Permeability:  2.746175778156612e-05
Pgp-inhibitor:  0.256
Pgp-substrate:  0.032
Human Intestinal Absorption (HIA):  0.125
20% Bioavailability (F20%):  0.113
30% Bioavailability (F30%):  0.019

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.907
Plasma Protein Binding (PPB):  84.27931213378906%
Volume Distribution (VD):  1.731
Pgp-substrate:  14.131301879882812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.92
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.669
CYP2C9-inhibitor:  0.067
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.104
CYP3A4-inhibitor:  0.684
CYP3A4-substrate:  0.396

ADMET: Excretion

Clearance (CL):  2.506
Half-life (T1/2):  0.226

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.27
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.24
Rat Oral Acute Toxicity:  0.226
Maximum Recommended Daily Dose:  0.742
Skin Sensitization:  0.088
Carcinogencity:  0.107
Eye Corrosion:  0.014
Eye Irritation:  0.31
Respiratory Toxicity:  0.96

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  Natural Product: NPC219953

Natural Product ID:  NPC219953
Common Name*:   XJXDJAQAAAVDCT-RHOFUAETSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XJXDJAQAAAVDCT-RHOFUAETSA-N
Standard InCHI:  InChI=1S/C20H28O5/c1-5-17(4)9-10-19(23)12(11-17)13(21)20(24)14-16(2,3)7-6-8-18(14,19)15(22)25-20/h5,11,13-14,21,23-24H,1,6-10H2,2-4H3/t13-,14+,17+,18+,19-,20-/m1/s1
SMILES:  C=C[C@@]1(C)CC[C@]2(C(=C1)[C@H]([C@@]1([C@H]3C(C)(C)CCC[C@]23C(=O)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   57396736
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
NPO27746 Taxus mairei Species Taxaceae Eukaryota stem bark n.a. n.a. PMID[11473432]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota Fruits n.a. n.a. PMID[12713411]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[16124776]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[17907781]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[18804027]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[19646881]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO6850 Typha domingensis Species Typhaceae Eukaryota n.a. aerial part n.a. PMID[21417376]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. Urup Island (4557,9 N; 15044,9 E; depth 66 m) 2008-AUG PMID[21848268]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[21848268]
NPO30074 Diplodia cupressi Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[22124378]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota nut shell n.a. n.a. PMID[23044367]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. PMID[24460410]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[2553871]
NPO40798 Botrysphaeria laricina Species n.a. n.a. n.a. n.a. n.a. PMID[28609099]
NPO40584 Aspergillus taichungensis (IBT 19404) Strain Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[30995043]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[32058711]
NPO17226 Burkholderia pyrrocinia Species Burkholderiaceae Bacteria n.a. n.a. n.a. PMID[4955234]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[8557595]
NPO27746 Taxus mairei Species Taxaceae Eukaryota Roots n.a. n.a. PMID[8991951]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9644081]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24730 Lactarius deliciosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25492 Botryllus leachi Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18463 Plectocephalus chilensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3756 Munronia delavayi Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6302 Licaria armeniaca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24461 Clusia sandiensis Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2609 Neonectria candida Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18706 Anemone thalictroides Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24607 Goniothalamus dolichocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25277 Seiridium cupressi Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23894 Pulicaria insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25775 Dasystenella acanthina Species Primnoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3721 Achyranthes obtusifolia Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20264 Moonia heterophylla n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14189 Osmundaria spiralis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1897 Ephedra aphylla Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25441 Desmodium pulchellu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO291 Suillus bovinus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15482 Vanderbylia fraxinea Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2968 Anthopleura xanthogrammica Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24882 Erythrophleum chlorostachys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24566 Marasmiellus ramealis Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22152 Tecoma undulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27390 Vernonia brevifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO115 Eutreptia viridis Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25466 Lecanora sulphurella Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24802 Diploprion bifasciatum Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19333 Byssothecium obiones Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6130 Mammillaria magnimamma Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10870 Trichilia hirta Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6850 Typha domingensis Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23994 Ormosia macrophylla Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28460 Achyrocline tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4816 Cycas armstrongii Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25389 Allium angulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22618 Psolus eximius Species Psolidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17226 Burkholderia pyrrocinia Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3419 Quercus suber Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4293 Allium neapolitanum Species Amaryllidaceae 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
NPT440 Individual Protein Quinone oxidoreductase Mus musculus FC = 2.3 n.a. PMID[28609099]
NPT2 Others Unspecified IC50 > 50000.0 nM PMID[28609099]

☑ 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 NPC219953 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 NPC219953 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