Structure

Physi-Chem Properties

Molecular Weight:  448.1
Volume:  413.147
LogP:  1.593
LogD:  0.734
LogS:  -4.135
# Rotatable Bonds:  3
TPSA:  190.28
# H-Bond Aceptor:  11
# H-Bond Donor:  7
# Rings:  4
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.276
Synthetic Accessibility Score:  4.008
Fsp3:  0.286
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.235
MDCK Permeability:  7.040875971142668e-06
Pgp-inhibitor:  0.018
Pgp-substrate:  0.937
Human Intestinal Absorption (HIA):  0.288
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  91.8907241821289%
Volume Distribution (VD):  0.78
Pgp-substrate:  11.605158805847168%

ADMET: Metabolism

CYP1A2-inhibitor:  0.599
CYP1A2-substrate:  0.067
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.048
CYP2C9-inhibitor:  0.313
CYP2C9-substrate:  0.561
CYP2D6-inhibitor:  0.367
CYP2D6-substrate:  0.174
CYP3A4-inhibitor:  0.168
CYP3A4-substrate:  0.016

ADMET: Excretion

Clearance (CL):  6.864
Half-life (T1/2):  0.889

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.127
Drug-inuced Liver Injury (DILI):  0.979
AMES Toxicity:  0.828
Rat Oral Acute Toxicity:  0.101
Maximum Recommended Daily Dose:  0.056
Skin Sensitization:  0.854
Carcinogencity:  0.086
Eye Corrosion:  0.003
Eye Irritation:  0.891
Respiratory Toxicity:  0.058

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  Natural Product: NPC268632

Natural Product ID:  NPC268632
Common Name*:   OXGUCUVFOIWWQJ-KHCWRDDVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OXGUCUVFOIWWQJ-KHCWRDDVSA-N
Standard InCHI:  InChI=1S/C21H20O11/c1-7-15(26)17(28)18(29)21(30-7)32-20-16(27)14-12(25)5-9(22)6-13(14)31-19(20)8-2-3-10(23)11(24)4-8/h2-7,15,17-18,21-26,28-29H,1H3/t7-,15-,17+,18-,21+/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(c(c1)O)O)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11972444
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003531] Flavonoid-3-O-glycosides

*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
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39730000707]
NPO12926 Dendrospora tenella Species n.a. Eukaryota n.a. n.a. n.a. PMID[10217713]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11473412]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[15730255]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. root n.a. PMID[15730255]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[16724861]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. PMID[17315967]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18491868]
NPO26507 Galenia africana Species Aizoaceae Eukaryota leaf n.a. n.a. PMID[20035557]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. atlantic-forest-soil n.a. PMID[20450206]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[21302965]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26566007]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. PMID[27684202]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[7288445]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7310 Corchorus trilocularis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13091 Helianthus ciliaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26561 Micromeria pineolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7447 Nemalion vermiculare Species Liagoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26374 Alangium premnifolium Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28041 Scaevola taccada Species Goodeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25995 Laurencia distichophylla Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26900 Vallota purpurea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12431 Cytospora rhizophorae Species Valsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13518 Senecio stabianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26507 Galenia africana Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13919 Agathis microstachya Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26184 Diphasia angolensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26584 Gnidia lamprantha Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25949 Streptomyces griseovariabilis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26406 Saussurea carthamoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4425 Delphinium honanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7310 Corchorus trilocularis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25896 Bragantia wallichii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20658 Lonicera caerulea Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12926 Dendrospora tenella Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13415 Securigera coronilla Species Romaleidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10049 Coleophoma empetri Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10422 Penicillium thymicola Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26161 Globba malaccensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12245 Lasiosiphon burchellii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2898 Quercus sessiliflora Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26624 Ilex amara Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26052 Swertia delavayi Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26023 Angelica tarokoensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25739 Erysimum odoratum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26950 Maba buxifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12771 Eucalyptus alba Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6238 Pseudo-nitzschia multiseries Species Bacillariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26607 Colobocentrotus atratus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26319 Solanum acaule Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13625 Salacia beddomei Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26287 Spodoptera eridania Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11384 Tibouchina semidecandra Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25792 Delphinium andersoni Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26806 Nidula candida Species Nidulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25923 Vismia jefensis Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9097 Solanum hypomalacophyllum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13091 Helianthus ciliaris Species Asteraceae 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 NPC268632 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 NPC268632 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