Structure

Physi-Chem Properties

Molecular Weight:  427.31
Volume:  462.224
LogP:  4.11
LogD:  3.884
LogS:  -4.581
# Rotatable Bonds:  2
TPSA:  69.89
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.634
Synthetic Accessibility Score:  5.109
Fsp3:  0.852
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.777
MDCK Permeability:  7.242580522870412e-06
Pgp-inhibitor:  0.943
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.96
30% Bioavailability (F30%):  0.033

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.788
Plasma Protein Binding (PPB):  86.2900390625%
Volume Distribution (VD):  0.821
Pgp-substrate:  8.499736785888672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.033
CYP1A2-substrate:  0.322
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.676
CYP2C9-inhibitor:  0.05
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.234
CYP3A4-inhibitor:  0.883
CYP3A4-substrate:  0.36

ADMET: Excretion

Clearance (CL):  13.733
Half-life (T1/2):  0.376

ADMET: Toxicity

hERG Blockers:  0.272
Human Hepatotoxicity (H-HT):  0.131
Drug-inuced Liver Injury (DILI):  0.228
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.596
Maximum Recommended Daily Dose:  0.935
Skin Sensitization:  0.808
Carcinogencity:  0.794
Eye Corrosion:  0.117
Eye Irritation:  0.056
Respiratory Toxicity:  0.983

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

  Natural Product: NPC193947

Natural Product ID:  NPC193947
Common Name*:   NDQADFJKKHDIGT-DMIHGHCOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NDQADFJKKHDIGT-DMIHGHCOSA-N
Standard InCHI:  InChI=1S/C15H21BrO/c1-3-5-7-10-13-11-8-6-9-12-14(16)15(4-2)17-13/h1,5,7,9,12-15H,4,6,8,10-11H2,2H3/b7-5-,12-9?/t13-,14+,15+/m1/s1
SMILES:  C#C/C=CC[C@@H]1CCCC=C[C@@H]([C@H](CC)O1)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001167] Dialkyl ethers

*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
NPO28122 Senecio chionophilus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15387646]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28645 Chondria armata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28645 Chondria armata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27917 Ulmus campestris Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28505 Arum palaestinum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28279 Mikania cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28030 Polysiphonia nigra Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28227 Prunus speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27889 Anacyclus monanthos Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28403 Comanthus bennetti Species Comatulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28420 Guizotia scabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27969 Elvira biflora Species Trochilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28156 Nezara viridula Species Pentatomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28122 Senecio chionophilus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28082 Corydalis tashiroi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28522 Flustra denticulata Species Flustridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28331 Astragalus siculus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28105 Coriolopsis gallica Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28493 Euphorbia cuneata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27701 Otholobium glandulosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21945 Amomum melegueta Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28539 Xestospongia vanilla Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27768 Terminalia brachystemma Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28314 Hakea trifurcata Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27849 Raoulia australis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28645 Chondria armata Species Rhodomelaceae 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 NPC193947 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 NPC193947 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