Structure

Physi-Chem Properties

Molecular Weight:  297.95
Volume:  232.103
LogP:  2.709
LogD:  1.717
LogS:  -2.564
# Rotatable Bonds:  5
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.425
Synthetic Accessibility Score:  4.581
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  3
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.595
MDCK Permeability:  2.0862962628598325e-05
Pgp-inhibitor:  0.013
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.935
Plasma Protein Binding (PPB):  70.33831024169922%
Volume Distribution (VD):  2.41
Pgp-substrate:  26.097566604614258%

ADMET: Metabolism

CYP1A2-inhibitor:  0.462
CYP1A2-substrate:  0.875
CYP2C19-inhibitor:  0.303
CYP2C19-substrate:  0.869
CYP2C9-inhibitor:  0.118
CYP2C9-substrate:  0.535
CYP2D6-inhibitor:  0.096
CYP2D6-substrate:  0.73
CYP3A4-inhibitor:  0.173
CYP3A4-substrate:  0.553

ADMET: Excretion

Clearance (CL):  0.778
Half-life (T1/2):  0.67

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.224
Drug-inuced Liver Injury (DILI):  0.193
AMES Toxicity:  0.747
Rat Oral Acute Toxicity:  0.129
Maximum Recommended Daily Dose:  0.394
Skin Sensitization:  0.957
Carcinogencity:  0.779
Eye Corrosion:  0.982
Eye Irritation:  0.984
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC477790

Natural Product ID:  NPC477790
Common Name*:   8-Bromo-6,7-dichloro-3,7-dimethylocta-2,4-dienal
IUPAC Name:   (2E,4E)-8-bromo-6,7-dichloro-3,7-dimethylocta-2,4-dienal
Synonyms:  
Standard InCHIKey:  SGOCPOPBYBKLBI-SALQQRKASA-N
Standard InCHI:  InChI=1S/C10H13BrCl2O/c1-8(5-6-14)3-4-9(12)10(2,13)7-11/h3-6,9H,7H2,1-2H3/b4-3+,8-5+
SMILES:  C/C(=C\C=O)/C=C/C(C(C)(CBr)Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16215041
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:0002433] Alpha,beta-unsaturated aldehydes
              • [CHEMONTID:0002436] Enals

*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
NPO19499 Plocamium corallorhiza Species Plocamiaceae Eukaryota n.a. South African n.a. PMID[17343409]
NPO19499 Plocamium corallorhiza Species Plocamiaceae 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
NPT27 Others Unspecified IC50 = 64800 nM PMID[17343409]

☑ 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 NPC477790 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
0.7222 Intermediate Similarity NPC473533
0.7018 Intermediate Similarity NPC477789
0.6792 Remote Similarity NPC323278
0.6545 Remote Similarity NPC208936
0.6538 Remote Similarity NPC8416
0.6481 Remote Similarity NPC12319
0.6481 Remote Similarity NPC101147
0.6481 Remote Similarity NPC18205
0.6364 Remote Similarity NPC259702
0.6346 Remote Similarity NPC75204
0.6296 Remote Similarity NPC33761
0.623 Remote Similarity NPC30433
0.6226 Remote Similarity NPC254764
0.6226 Remote Similarity NPC279300
0.6154 Remote Similarity NPC72258
0.6071 Remote Similarity NPC469969
0.6071 Remote Similarity NPC33489
0.6 Remote Similarity NPC55269
0.5965 Remote Similarity NPC67920
0.5965 Remote Similarity NPC287397
0.5965 Remote Similarity NPC298710
0.5962 Remote Similarity NPC146507
0.5926 Remote Similarity NPC201753
0.5909 Remote Similarity NPC208749
0.5909 Remote Similarity NPC281986
0.5909 Remote Similarity NPC321568
0.5909 Remote Similarity NPC22019
0.5846 Remote Similarity NPC188789
0.5789 Remote Similarity NPC107849
0.5769 Remote Similarity NPC144407
0.5758 Remote Similarity NPC469967
0.5714 Remote Similarity NPC101811
0.566 Remote Similarity NPC310810
0.5652 Remote Similarity NPC477430

  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 NPC477790 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