Structure

Physi-Chem Properties

Molecular Weight:  168.08
Volume:  174.125
LogP:  1.479
LogD:  1.294
LogS:  -1.911
# Rotatable Bonds:  3
TPSA:  27.69
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  1.364
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.47
MDCK Permeability:  2.9830785933881998e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.071

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.938
Plasma Protein Binding (PPB):  58.06040573120117%
Volume Distribution (VD):  1.294
Pgp-substrate:  20.115249633789062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.936
CYP1A2-substrate:  0.952
CYP2C19-inhibitor:  0.605
CYP2C19-substrate:  0.915
CYP2C9-inhibitor:  0.04
CYP2C9-substrate:  0.834
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.92
CYP3A4-inhibitor:  0.118
CYP3A4-substrate:  0.581

ADMET: Excretion

Clearance (CL):  8.325
Half-life (T1/2):  0.866

ADMET: Toxicity

hERG Blockers:  0.11
Human Hepatotoxicity (H-HT):  0.084
Drug-inuced Liver Injury (DILI):  0.185
AMES Toxicity:  0.115
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.809
Carcinogencity:  0.644
Eye Corrosion:  0.889
Eye Irritation:  0.957
Respiratory Toxicity:  0.16

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  Natural Product: NPC175069

Natural Product ID:  NPC175069
Common Name*:   CRUILBNAQILVHZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CRUILBNAQILVHZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H12O3/c1-10-7-5-4-6-8(11-2)9(7)12-3/h4-6H,1-3H3
SMILES:  COc1cccc(c1OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12462
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002341] Phenol ethers
        • [CHEMONTID:0000138] Anisoles

*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
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10843584]
NPO27252 Iochroma australe Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[12027740]
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO26782 Dendrilla membranosa Species Darwinellidae Eukaryota n.a. antarctic n.a. PMID[15270575]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[15497934]
NPO30570 Tetrapanax papyriferus Species Araliaceae Eukaryota n.a. fruit n.a. PMID[16378372]
NPO30570 Tetrapanax papyriferus Species Araliaceae Eukaryota n.a. flower n.a. PMID[16378372]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[30407007]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26163 Anisodus tanguticus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30570 Tetrapanax papyriferus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25821 Delphinium cashmerianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25717 Maytenus hookeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2039 Callerya cinerea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29051 Ranunculus acris Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25717 Maytenus hookeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25821 Delphinium cashmerianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26163 Anisodus tanguticus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25717 Maytenus hookeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30570 Tetrapanax papyriferus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26352 Heuchera cylindrica Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26109 Pilocarpus spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26408 Melanophryniscus moreirae Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26535 Balanus glandula Species Balanidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24378 Osmanthus heterophyllus Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3346 Piper sanctum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18292 Guarea trichilioides Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26678 Calea pilosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25849 Streptomyces lomondensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29051 Ranunculus acris Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11845 Petrorhagia dubia Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25793 Gremmeniella abietina Species Helotiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26453 Prunus lusitanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26053 Pluchea suaveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26377 Amelanchier vulgaris Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26563 Alectoria japonica Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26289 Lecidella chodati Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27377 Diaporthe helianthi Species Diaporthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26186 Stereocaulon leprocauloides Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26026 Vitis silvestris Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26884 Helichrysum davenportii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13781 Eremostachys moluccelloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25741 Aster ageratoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25717 Maytenus hookeri Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26430 Aplysina laevis Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26754 Stevia connata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26952 Cineraria geifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27252 Iochroma australe Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25976 Dendronephthya gigantea Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7214 Bufotes viridis Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26244 Panax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25821 Delphinium cashmerianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2344 Carlina acanthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26782 Dendrilla membranosa Species Darwinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO137 Nepeta multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26163 Anisodus tanguticus Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26213 Tephrosia vogelii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2039 Callerya cinerea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25997 Senecio rupestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14466 Penicillium olsonii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26903 Plectranthus purpuratus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19823 Vicia benghalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26078 Mussaenda parviflora Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25952 Lastrea thelypteris n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25926 Tephrosia pumila Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26135 Walsura tubulata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25873 Thaminophyllum multiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26980 Halocarpus biformis Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26727 Eremocarpus setiger n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26625 Stichopus chloronotus Species Stichopodidae 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 NPC175069 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 NPC175069 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