Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  257.271
LogP:  3.081
LogD:  2.846
LogS:  -4.392
# Rotatable Bonds:  1
TPSA:  32.76
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.561
Synthetic Accessibility Score:  4.816
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.407
MDCK Permeability:  2.2657910449197516e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.849
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.664
Plasma Protein Binding (PPB):  59.66908264160156%
Volume Distribution (VD):  1.327
Pgp-substrate:  30.9605712890625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.094
CYP1A2-substrate:  0.497
CYP2C19-inhibitor:  0.073
CYP2C19-substrate:  0.853
CYP2C9-inhibitor:  0.06
CYP2C9-substrate:  0.195
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.577
CYP3A4-inhibitor:  0.111
CYP3A4-substrate:  0.308

ADMET: Excretion

Clearance (CL):  8.268
Half-life (T1/2):  0.459

ADMET: Toxicity

hERG Blockers:  0.067
Human Hepatotoxicity (H-HT):  0.404
Drug-inuced Liver Injury (DILI):  0.467
AMES Toxicity:  0.049
Rat Oral Acute Toxicity:  0.133
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.151
Carcinogencity:  0.407
Eye Corrosion:  0.215
Eye Irritation:  0.695
Respiratory Toxicity:  0.962

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC28076

Natural Product ID:  NPC28076
Common Name*:   DHOMMAYDBREASS-XLWJZTARSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DHOMMAYDBREASS-XLWJZTARSA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-9(2)15-8-5-10(3)11-6-7-14(4,16)12(11)13(15)17-15/h9,11-13,16H,3,5-8H2,1-2,4H3/t11-,12+,13-,14-,15-/m1/s1
SMILES:  CC(C)[C@]12CCC(=C)[C@H]3CC[C@](C)([C@@H]3[C@H]1O2)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:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota roots northern Saudi desert n.a. PMID[10924184]
NPO6831 Commiphora opobalsamum Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[18177010]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8297 Hydnellum caeruleum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4463 Cytisus canariensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9639 Prunus puddum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25831 Siphonoglossa sessilis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3693 Calpurnia aurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9883 Allium giganteum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6022 Cytisus supinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8985 Gazania rigens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6831 Commiphora opobalsamum Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24891 Elmerina caryae Species Aporpiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5284 Ramalina hierrensis Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1586 Gorgonocephalus chilensis Species Gorgonocephalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5886 Fossombronia alaskana Species Fossombroniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8810 Pinus austriaca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29336 Corynandra chelidonii Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8297 Hydnellum caeruleum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10085 Aspergillus varians Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9036 Dipteryx lacunifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2328 Lagochilus setulosus Species Lamiaceae 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 NPC28076 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 NPC28076 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