Structure

Physi-Chem Properties

Molecular Weight:  538.09
Volume:  521.816
LogP:  5.229
LogD:  2.266
LogS:  -4.321
# Rotatable Bonds:  3
TPSA:  181.8
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  6
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.177
Synthetic Accessibility Score:  3.104
Fsp3:  0.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.568
MDCK Permeability:  5.42930274605169e-06
Pgp-inhibitor:  0.032
Pgp-substrate:  0.067
Human Intestinal Absorption (HIA):  0.053
20% Bioavailability (F20%):  0.456
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  97.39739227294922%
Volume Distribution (VD):  0.402
Pgp-substrate:  1.5686227083206177%

ADMET: Metabolism

CYP1A2-inhibitor:  0.827
CYP1A2-substrate:  0.08
CYP2C19-inhibitor:  0.532
CYP2C19-substrate:  0.028
CYP2C9-inhibitor:  0.627
CYP2C9-substrate:  0.841
CYP2D6-inhibitor:  0.094
CYP2D6-substrate:  0.248
CYP3A4-inhibitor:  0.161
CYP3A4-substrate:  0.043

ADMET: Excretion

Clearance (CL):  4.1
Half-life (T1/2):  0.764

ADMET: Toxicity

hERG Blockers:  0.094
Human Hepatotoxicity (H-HT):  0.101
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.269
Rat Oral Acute Toxicity:  0.692
Maximum Recommended Daily Dose:  0.638
Skin Sensitization:  0.904
Carcinogencity:  0.06
Eye Corrosion:  0.003
Eye Irritation:  0.901
Respiratory Toxicity:  0.021

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  Natural Product: NPC302760

Natural Product ID:  NPC302760
Common Name*:   AQWPITGEZPPXTJ-SPFKKGSWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AQWPITGEZPPXTJ-SPFKKGSWSA-N
Standard InCHI:  InChI=1S/C10H20O6/c1-12-5-6-7(13-2)8(14-3)9(15-4)10(11)16-6/h6-11H,5H2,1-4H3/t6-,7-,8+,9-,10+/m1/s1
SMILES:  COC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O)O1)OC)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   111162
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

*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
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. DOI[10.1246/bcsj.30.618]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. root n.a. PMID[14727919]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. leaf n.a. PMID[14727919]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. bark n.a. PMID[14727919]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. xylem n.a. PMID[14727919]
NPO29530 Kaempferia marginata Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[16309313]
NPO27743 Aaptos aaptos Species Suberitidae Eukaryota n.a. n.a. n.a. PMID[17716892]
NPO29381 Trichilia rubescens Species Meliaceae Eukaryota leaves Kibale National Park, Uganda 2000-2001 PMID[19299148]
NPO28864 Nauclea officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO27743 Aaptos aaptos Species Suberitidae Eukaryota n.a. South China Sea n.a. PMID[25211032]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. PMID[27466882]
NPO4055 Aspergillus unguis Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31117521]
NPO29530 Kaempferia marginata Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[31873014]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28949 Croton cumingii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28864 Nauclea officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO29530 Kaempferia marginata Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4055 Aspergillus unguis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29344 Parabenzoin trilobum n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO28805 Thymus piperella Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28949 Croton cumingii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28864 Nauclea officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28864 Nauclea officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28949 Croton cumingii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28824 Forsteronia refracta Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28898 Grewia mollis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29363 Aconitum nevadense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29400 Conocephalum japonicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26192 Cordylanthus kingii Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29510 Aulacocephalus temmincki Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29446 Stevia polycephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28918 Ophiolepis superba Species Ophiolepididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29530 Kaempferia marginata Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29154 Heliotropium floridum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29047 Disynaphia halimifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28864 Nauclea officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29292 Teucrium depressum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29276 Juglans nigra Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28971 Bersama yangambiensis Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27269 Annona impressivenia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29189 Castanopsis sclerophylla Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4055 Aspergillus unguis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29415 Hovenia acerba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25981 Crinipellis scabella Species Marasmiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13818 Narcissus concolor Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27743 Aaptos aaptos Species Suberitidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3744 Polycephalomyces nipponicus Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28784 Alseodaphne corneri Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29203 Gymnocarpium robertianum Species Cystopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9157 Rubrivivax gelatinosus Species n.a. Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4244 Doodia picta Species Blechnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29488 Sophora angustifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29142 Kaunia saltensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29450 Streptomyces parvisporogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29344 Parabenzoin trilobum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28805 Thymus piperella Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3340 Fridericia chica Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29068 Papilio phorcas Species Papilionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28937 Heterotheca grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1245 Eunicella cavolinii Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29242 Salvia dorrii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28845 Eragrostis viscosa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29127 Cystophora scalaris Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29225 Oncoba echinata Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29381 Trichilia rubescens Species Meliaceae 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 NPC302760 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 NPC302760 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