Structure

Physi-Chem Properties

Molecular Weight:  250.01
Volume:  210.738
LogP:  4.787
LogD:  4.084
LogS:  -4.949
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.505
Synthetic Accessibility Score:  4.167
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.422
MDCK Permeability:  2.1376143195084296e-05
Pgp-inhibitor:  0.073
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.16
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.391
Plasma Protein Binding (PPB):  96.08863067626953%
Volume Distribution (VD):  2.656
Pgp-substrate:  5.697394371032715%

ADMET: Metabolism

CYP1A2-inhibitor:  0.902
CYP1A2-substrate:  0.37
CYP2C19-inhibitor:  0.671
CYP2C19-substrate:  0.855
CYP2C9-inhibitor:  0.256
CYP2C9-substrate:  0.626
CYP2D6-inhibitor:  0.544
CYP2D6-substrate:  0.322
CYP3A4-inhibitor:  0.845
CYP3A4-substrate:  0.268

ADMET: Excretion

Clearance (CL):  3.608
Half-life (T1/2):  0.158

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.525
Drug-inuced Liver Injury (DILI):  0.078
AMES Toxicity:  0.118
Rat Oral Acute Toxicity:  0.073
Maximum Recommended Daily Dose:  0.045
Skin Sensitization:  0.558
Carcinogencity:  0.332
Eye Corrosion:  0.969
Eye Irritation:  0.989
Respiratory Toxicity:  0.602

Download Data

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

  Natural Product: NPC469969

Natural Product ID:  NPC469969
Common Name*:   3-Bromomethyl-3-Chloro-7-Methyl-Octa-1,6-Diene
IUPAC Name:   3-(bromomethyl)-3-chloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  AXQZHNCLKGWAAS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H16BrCl/c1-4-10(12,8-11)7-5-6-9(2)3/h4,6H,1,5,7-8H2,2-3H3
SMILES:  BrCC(CCC=C(C)C)(C=C)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL139678
PubChem CID:   392485
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO32563 portieria hornemannii Species Rhizophyllidaceae Eukaryota n.a. Madagascar n.a. PMID[16643029]
NPO32563 portieria hornemannii Species Rhizophyllidaceae Eukaryota n.a. n.a. n.a. PMID[7996553]

☑ 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
NPT3804 Cell Line Human Tumor Cell lines GI50 = 33100.0 nM PMID[564014]
NPT3804 Cell Line Human Tumor Cell lines TGI > 100000.0 nM PMID[564014]
NPT3804 Cell Line Human Tumor Cell lines LC50 > 100000.0 nM PMID[564014]

☑ 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 NPC469969 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
0.9 High Similarity NPC259702
0.85 High Similarity NPC55269
0.8462 Intermediate Similarity NPC201753
0.8095 Intermediate Similarity NPC107849
0.8049 Intermediate Similarity NPC101811
0.75 Intermediate Similarity NPC160588
0.7179 Intermediate Similarity NPC206088
0.7174 Intermediate Similarity NPC473533
0.7111 Intermediate Similarity NPC474773
0.6981 Remote Similarity NPC469967
0.6957 Remote Similarity NPC99746
0.675 Remote Similarity NPC66577
0.6667 Remote Similarity NPC138113
0.6667 Remote Similarity NPC51086
0.6667 Remote Similarity NPC469962
0.6585 Remote Similarity NPC213749
0.6531 Remote Similarity NPC159420
0.6512 Remote Similarity NPC282119
0.65 Remote Similarity NPC60288
0.6383 Remote Similarity NPC180409
0.6346 Remote Similarity NPC469971
0.625 Remote Similarity NPC115959
0.625 Remote Similarity NPC123965
0.6222 Remote Similarity NPC45727
0.6222 Remote Similarity NPC48638
0.6136 Remote Similarity NPC92224
0.6098 Remote Similarity NPC16561
0.6071 Remote Similarity NPC477790
0.6047 Remote Similarity NPC99088
0.6047 Remote Similarity NPC305759
0.6047 Remote Similarity NPC173592
0.6 Remote Similarity NPC64176
0.6 Remote Similarity NPC76145
0.6 Remote Similarity NPC288991
0.6 Remote Similarity NPC34764
0.6 Remote Similarity NPC262789
0.6 Remote Similarity NPC138325
0.6 Remote Similarity NPC190810
0.5957 Remote Similarity NPC183670
0.5952 Remote Similarity NPC3649
0.5952 Remote Similarity NPC471327
0.5952 Remote Similarity NPC100879
0.587 Remote Similarity NPC229262
0.587 Remote Similarity NPC139717
0.587 Remote Similarity NPC297643
0.587 Remote Similarity NPC239039
0.587 Remote Similarity NPC266298
0.5854 Remote Similarity NPC34671
0.5833 Remote Similarity NPC218918
0.5833 Remote Similarity NPC120926
0.5833 Remote Similarity NPC144023
0.575 Remote Similarity NPC10183
0.5714 Remote Similarity NPC51758
0.5714 Remote Similarity NPC68889
0.5714 Remote Similarity NPC108494
0.5714 Remote Similarity NPC67761
0.5714 Remote Similarity NPC180871
0.5714 Remote Similarity NPC177470
0.5714 Remote Similarity NPC194586
0.5714 Remote Similarity NPC88079
0.5714 Remote Similarity NPC209279
0.5667 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 NPC469969 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
0.6 Remote Similarity NPD319 Phase 1

  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