Structure

Physi-Chem Properties

Molecular Weight:  373.85
Volume:  225.588
LogP:  4.787
LogD:  3.123
LogS:  -5.376
# Rotatable Bonds:  6
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.477
Synthetic Accessibility Score:  2.953
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.427
MDCK Permeability:  9.40504833124578e-06
Pgp-inhibitor:  0.805
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.2
30% Bioavailability (F30%):  0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.978
Plasma Protein Binding (PPB):  96.8297348022461%
Volume Distribution (VD):  0.999
Pgp-substrate:  7.215554237365723%

ADMET: Metabolism

CYP1A2-inhibitor:  0.924
CYP1A2-substrate:  0.516
CYP2C19-inhibitor:  0.882
CYP2C19-substrate:  0.629
CYP2C9-inhibitor:  0.832
CYP2C9-substrate:  0.645
CYP2D6-inhibitor:  0.034
CYP2D6-substrate:  0.156
CYP3A4-inhibitor:  0.288
CYP3A4-substrate:  0.236

ADMET: Excretion

Clearance (CL):  0.985
Half-life (T1/2):  0.164

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.95
Drug-inuced Liver Injury (DILI):  0.928
AMES Toxicity:  0.546
Rat Oral Acute Toxicity:  0.407
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.963
Carcinogencity:  0.911
Eye Corrosion:  0.979
Eye Irritation:  0.99
Respiratory Toxicity:  0.979

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Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC473674

Natural Product ID:  NPC473674
Common Name*:   1,1,2-Tribromonon-1-En-3-One
IUPAC Name:   1,1,2-tribromonon-1-en-3-one
Synonyms:  
Standard InCHIKey:  MUTVKAVCFPCTJE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H13Br3O/c1-2-3-4-5-6-7(13)8(10)9(11)12/h2-6H2,1H3
SMILES:  CCCCCCC(=O)C(=C(Br)Br)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL448764
PubChem CID:   44583903
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds
            • [CHEMONTID:0003672] Alpha,beta-unsaturated ketones
              • [CHEMONTID:0003674] Alpha-branched alpha,beta-unsaturated ketones

*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
NPO14524 Delisea pulchra Species Bonnemaisoniaceae Eukaryota n.a. n.a. n.a. PMID[16933872]
NPO14524 Delisea pulchra Species Bonnemaisoniaceae 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
NPT453 Cell Line HT-1080 Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT1034 Cell Line Lu1 Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT91 Cell Line KB Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT168 Cell Line P388 Mus musculus ED50 > 5.0 ug ml-1 PMID[460181]
NPT762 Cell Line A-431 Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT858 Cell Line LNCaP Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 > 20.0 ug ml-1 PMID[460181]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 > 20.0 ug ml-1 PMID[460181]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 10.0 mm PMID[460181]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 5.0 mm PMID[460181]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Activity > 50.0 % PMID[460181]
NPT2 Others Unspecified IC50 >= 200000.0 nM PMID[460181]

☑ 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 NPC473674 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
0.7255 Intermediate Similarity NPC473784
0.6977 Remote Similarity NPC220061
0.65 Remote Similarity NPC42403
0.65 Remote Similarity NPC196434
0.65 Remote Similarity NPC79887
0.65 Remote Similarity NPC29561
0.65 Remote Similarity NPC222997
0.65 Remote Similarity NPC153439
0.65 Remote Similarity NPC4962
0.65 Remote Similarity NPC221192
0.6341 Remote Similarity NPC168982
0.625 Remote Similarity NPC295442
0.625 Remote Similarity NPC198118
0.625 Remote Similarity NPC38859
0.619 Remote Similarity NPC76608
0.619 Remote Similarity NPC268596
0.619 Remote Similarity NPC225318
0.619 Remote Similarity NPC149101
0.619 Remote Similarity NPC16578
0.6154 Remote Similarity NPC145311
0.6098 Remote Similarity NPC158107
0.6038 Remote Similarity NPC474391
0.6 Remote Similarity NPC25771
0.5926 Remote Similarity NPC477458
0.5897 Remote Similarity NPC66624
0.5833 Remote Similarity NPC48930
0.58 Remote Similarity NPC292463
0.5769 Remote Similarity NPC236355
0.5769 Remote Similarity NPC4079
0.5769 Remote Similarity NPC100380
0.5769 Remote Similarity NPC14917
0.575 Remote Similarity NPC79591
0.5745 Remote Similarity NPC155880
0.5745 Remote Similarity NPC92863
0.5741 Remote Similarity NPC116906
0.5714 Remote Similarity NPC474141
0.566 Remote Similarity NPC324812
0.5652 Remote Similarity NPC301919
0.5636 Remote Similarity NPC236623

  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 NPC473674 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
NPD

  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