Structure

Physi-Chem Properties

Molecular Weight:  283.97
Volume:  225.949
LogP:  5.272
LogD:  3.707
LogS:  -5.325
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.5
Synthetic Accessibility Score:  4.197
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:  -4.54
MDCK Permeability:  2.282106834172737e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.379
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.392
Plasma Protein Binding (PPB):  97.75108337402344%
Volume Distribution (VD):  3.898
Pgp-substrate:  4.656394958496094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.967
CYP1A2-substrate:  0.63
CYP2C19-inhibitor:  0.767
CYP2C19-substrate:  0.819
CYP2C9-inhibitor:  0.334
CYP2C9-substrate:  0.163
CYP2D6-inhibitor:  0.18
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.52
CYP3A4-substrate:  0.277

ADMET: Excretion

Clearance (CL):  9.699
Half-life (T1/2):  0.091

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.814
Drug-inuced Liver Injury (DILI):  0.737
AMES Toxicity:  0.311
Rat Oral Acute Toxicity:  0.265
Maximum Recommended Daily Dose:  0.131
Skin Sensitization:  0.66
Carcinogencity:  0.568
Eye Corrosion:  0.98
Eye Irritation:  0.98
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC259702

Natural Product ID:  NPC259702
Common Name*:   (S)-3-Bromomethyl-2,3-Dichloro-7-Methyl-Octa-1,6-Diene
IUPAC Name:   (3S)-3-(bromomethyl)-2,3-dichloro-7-methylocta-1,6-diene
Synonyms:  
Standard InCHIKey:  YHCNATPUYZXDQB-SNVBAGLBSA-N
Standard InCHI:  InChI=1S/C10H15BrCl2/c1-8(2)5-4-6-10(13,7-11)9(3)12/h5H,3-4,6-7H2,1-2H3/t10-/m1/s1
SMILES:  BrC[C@@](C(=C)Cl)(CCC=C(C)C)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL139921
PubChem CID:   15345661
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 = 47000.0 nM PMID[523601]
NPT3804 Cell Line Human Tumor Cell lines TGI > 100000.0 nM PMID[523601]
NPT3804 Cell Line Human Tumor Cell lines LC50 > 100000.0 nM PMID[523601]

☑ 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 NPC259702 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
0.9474 High Similarity NPC55269
0.9 High Similarity NPC469969
0.9 High Similarity NPC107849
0.8462 Intermediate Similarity NPC201753
0.8049 Intermediate Similarity NPC101811
0.7556 Intermediate Similarity NPC473533
0.75 Intermediate Similarity NPC474773
0.7442 Intermediate Similarity NPC51086
0.7111 Intermediate Similarity NPC160588
0.7111 Intermediate Similarity NPC180409
0.6981 Remote Similarity NPC469962
0.6957 Remote Similarity NPC99746
0.6667 Remote Similarity NPC469967
0.6531 Remote Similarity NPC159420
0.6364 Remote Similarity NPC477790
0.6346 Remote Similarity NPC469971
0.6341 Remote Similarity NPC206088
0.619 Remote Similarity NPC213749
0.5952 Remote Similarity NPC66577
0.5854 Remote Similarity NPC115959
0.5854 Remote Similarity NPC123965
0.5854 Remote Similarity NPC138113
0.5778 Remote Similarity NPC92224
0.5778 Remote Similarity NPC282119
0.5714 Remote Similarity NPC60288
0.5652 Remote Similarity NPC34764
0.5652 Remote Similarity NPC190810
0.5652 Remote Similarity NPC76145

  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 NPC259702 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
0.5652 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