Structure

Physi-Chem Properties

Molecular Weight:  363.9
Volume:  247.869
LogP:  5.072
LogD:  4.2
LogS:  -5.651
# Rotatable Bonds:  6
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.453
Synthetic Accessibility Score:  4.836
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  3
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.458
MDCK Permeability:  2.474312532285694e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.406
30% Bioavailability (F30%):  0.132

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.651
Plasma Protein Binding (PPB):  97.21273040771484%
Volume Distribution (VD):  1.634
Pgp-substrate:  6.430361270904541%

ADMET: Metabolism

CYP1A2-inhibitor:  0.935
CYP1A2-substrate:  0.847
CYP2C19-inhibitor:  0.9
CYP2C19-substrate:  0.901
CYP2C9-inhibitor:  0.925
CYP2C9-substrate:  0.672
CYP2D6-inhibitor:  0.385
CYP2D6-substrate:  0.433
CYP3A4-inhibitor:  0.953
CYP3A4-substrate:  0.777

ADMET: Excretion

Clearance (CL):  1.906
Half-life (T1/2):  0.122

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.288
Drug-inuced Liver Injury (DILI):  0.371
AMES Toxicity:  0.148
Rat Oral Acute Toxicity:  0.287
Maximum Recommended Daily Dose:  0.602
Skin Sensitization:  0.639
Carcinogencity:  0.406
Eye Corrosion:  0.992
Eye Irritation:  0.978
Respiratory Toxicity:  0.951

Download Data

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

  Natural Product: NPC160588

Natural Product ID:  NPC160588
Common Name*:   (3S,6R)-6-Bromo-3-Bromomethyl-3,7-Dichloro-7-Methyl-Oct-1-Ene
IUPAC Name:   (3S,6R)-6-bromo-3-(bromomethyl)-3,7-dichloro-7-methyloct-1-ene
Synonyms:  
Standard InCHIKey:  OGRGXGGBTRUIDS-PSASIEDQSA-N
Standard InCHI:  InChI=1S/C10H16Br2Cl2/c1-4-10(14,7-11)6-5-8(12)9(2,3)13/h4,8H,1,5-7H2,2-3H3/t8-,10-/m1/s1
SMILES:  C=C[C@@](CC[C@H](C(C)(C)Cl)Br)(CBr)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL139528
PubChem CID:   392489
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0001516] Organochlorides

*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 = 26100.0 nM PMID[569207]
NPT3804 Cell Line Human Tumor Cell lines TGI = 77000.0 nM PMID[569207]
NPT3804 Cell Line Human Tumor Cell lines LC50 > 100000.0 nM PMID[569207]
NPT2752 Individual Protein DNA (cytosine-5)-methyltransferase 1 Homo sapiens Activity = 21.9 uM PMID[569208]

☑ 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 NPC160588 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
0.9268 High Similarity NPC99746
0.9 High Similarity NPC51086
0.8571 High Similarity NPC474773
0.8571 High Similarity NPC180409
0.75 Intermediate Similarity NPC469969
0.75 Intermediate Similarity NPC107849
0.7111 Intermediate Similarity NPC259702
0.7045 Intermediate Similarity NPC55269
0.6909 Remote Similarity NPC183031
0.6667 Remote Similarity NPC101811
0.6545 Remote Similarity NPC469962
0.6538 Remote Similarity NPC469971
0.6441 Remote Similarity NPC52966
0.6341 Remote Similarity NPC16561
0.625 Remote Similarity NPC469967
0.6222 Remote Similarity NPC201753
0.6 Remote Similarity NPC110214
0.5692 Remote Similarity NPC301725
0.5686 Remote Similarity NPC473533

  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 NPC160588 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