Structure

Physi-Chem Properties

Molecular Weight:  326.1
Volume:  308.023
LogP:  -0.022
LogD:  -0.537
LogS:  -0.978
# Rotatable Bonds:  5
TPSA:  136.68
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.341
Synthetic Accessibility Score:  3.633
Fsp3:  0.4
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:  -6.124
MDCK Permeability:  9.683067037258297e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.887
Human Intestinal Absorption (HIA):  0.93
20% Bioavailability (F20%):  0.926
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.348
Plasma Protein Binding (PPB):  64.0545425415039%
Volume Distribution (VD):  0.311
Pgp-substrate:  32.97542190551758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.18
CYP1A2-substrate:  0.024
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.129
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.128
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.012

ADMET: Excretion

Clearance (CL):  1.698
Half-life (T1/2):  0.826

ADMET: Toxicity

hERG Blockers:  0.081
Human Hepatotoxicity (H-HT):  0.376
Drug-inuced Liver Injury (DILI):  0.906
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.779
Carcinogencity:  0.057
Eye Corrosion:  0.004
Eye Irritation:  0.567
Respiratory Toxicity:  0.039

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  Natural Product: NPC75034

Natural Product ID:  NPC75034
Common Name*:   IFJZNZBKGRGNSP-WHPHWUKISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IFJZNZBKGRGNSP-WHPHWUKISA-N
Standard InCHI:  InChI=1S/C15H18O8/c16-7-10-11(17)12(18)13(19)15(23-10)22-9(14(20)21)6-8-4-2-1-3-5-8/h1-6,10-13,15-19H,7H2,(H,20,21)/t10-,11-,12+,13+,15-/m0/s1
SMILES:  c1ccc(cc1)C=C(C(=O)O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO27025 Erylus trisphaerus Species Geodiidae Eukaryota n.a. Dominican n.a. PMID[12713417]
NPO27007 Cunonia macrophylla Species Cunoniaceae Eukaryota n.a. New Caledonia n.a. PMID[15652581]
NPO26969 Sagittaria sagittifolia Species Alismataceae Eukaryota n.a. n.a. n.a. PMID[16499326]
NPO27576 Lysiana subfalcata Species Loranthaceae Eukaryota n.a. n.a. n.a. PMID[18222087]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[1955887]
NPO19202 Phaeolus schweinitzii Species Hymenochaetaceae Eukaryota fruits Tibetan Plateau n.a. PMID[23869482]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[2878063]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[7130988]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota bark n.a. n.a. PMID[7623034]
NPO26969 Sagittaria sagittifolia Species Alismataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27675 Platycarya strobilacea Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27237 Aucuba chinensis Species Garryaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27376 Curculigo pilosa Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27007 Cunonia macrophylla Species Cunoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27640 Sorbus tianschanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27840 Stephania elegans Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27675 Platycarya strobilacea Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9698 Parablechnum minus Species Blechnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26969 Sagittaria sagittifolia Species Alismataceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27007 Cunonia macrophylla Species Cunoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27640 Sorbus tianschanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27376 Curculigo pilosa Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27612 Peperomia vulcanica Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26969 Sagittaria sagittifolia Species Alismataceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27675 Platycarya strobilacea Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27640 Sorbus tianschanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19202 Phaeolus schweinitzii Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27800 Usnea undulata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27312 Citrus tangerina Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27696 Anolis lineatopus Species Iguanidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27440 Osteospermum muricatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27612 Peperomia vulcanica Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19173 Gleditsia caspica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15795 Humata pectinata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27597 Haplophyllum ramosissimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9698 Parablechnum minus Species Blechnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27788 Eupatorium areolare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27470 Centaurea huber-morathii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27274 Amsinckia tessellata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27138 Entada rheedei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27394 Sideritis euboea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27525 Saussurea amara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26882 Swertia swertopsis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22520 Felimida luteorosea Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27290 Carica dodecaphylla Species Caricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25349 Bistorta vivipara Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27453 Trichoderma koningi Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27237 Aucuba chinensis Species Garryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27419 Aurelia aurita Species Ulmaridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27076 Aspergillus mutabilis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27761 Aspalathus linearis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27732 Cynometra lujae Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27254 Utricularia australis Species Lentibulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26912 Premna tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27064 Taxus brevifolia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14449 Cedronella canariensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6917 Kali turgidum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27495 Sisyrinchium californicum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27345 Crocus minimus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26969 Sagittaria sagittifolia Species Alismataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27007 Cunonia macrophylla Species Cunoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15868 0stoc spongiaeforme Species 0stocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18100 Physalis edulis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29241 Macaranga peltata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27675 Platycarya strobilacea Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27576 Lysiana subfalcata Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27215 Gracilaria textorii Species Gracilariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27025 Erylus trisphaerus Species Geodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27099 Virgilia divaricata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27840 Stephania elegans Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27815 Sia ferox Species Stenopelmatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27376 Curculigo pilosa Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27050 Tsuga chinensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27712 Helichrysum mixtum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29217 Brickellia vernicosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27640 Sorbus tianschanica Species Rosaceae 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 NPC75034 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 NPC75034 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