Structure

Physi-Chem Properties

Molecular Weight:  395.84
Volume:  254.524
LogP:  4.989
LogD:  3.101
LogS:  -5.236
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.554
Synthetic Accessibility Score:  5.521
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:  -4.611
MDCK Permeability:  1.860023257904686e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.032
20% Bioavailability (F20%):  0.064
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.636
Plasma Protein Binding (PPB):  93.77368927001953%
Volume Distribution (VD):  1.951
Pgp-substrate:  3.742302894592285%

ADMET: Metabolism

CYP1A2-inhibitor:  0.919
CYP1A2-substrate:  0.755
CYP2C19-inhibitor:  0.908
CYP2C19-substrate:  0.896
CYP2C9-inhibitor:  0.801
CYP2C9-substrate:  0.68
CYP2D6-inhibitor:  0.865
CYP2D6-substrate:  0.468
CYP3A4-inhibitor:  0.953
CYP3A4-substrate:  0.607

ADMET: Excretion

Clearance (CL):  1.907
Half-life (T1/2):  0.549

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.25
Drug-inuced Liver Injury (DILI):  0.828
AMES Toxicity:  0.311
Rat Oral Acute Toxicity:  0.415
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.843
Carcinogencity:  0.471
Eye Corrosion:  0.992
Eye Irritation:  0.953
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: NPC183031

Natural Product ID:  NPC183031
Common Name*:   (1S,2S,4R,5R)-2-Bromo-1-(Bromomethyl)-1,4-Dichloro-5-(2-Chlorovinyl)-5-Methylcyclohexane
IUPAC Name:   (1S,2S,4R,5R)-2-bromo-1-(bromomethyl)-1,4-dichloro-5-[(E)-2-chloroethenyl]-5-methylcyclohexane
Synonyms:  
Standard InCHIKey:  MMMYYEWTEBVZHZ-MZXHXKKRSA-N
Standard InCHI:  InChI=1S/C10H13Br2Cl3/c1-9(2-3-13)5-10(15,6-11)7(12)4-8(9)14/h2-3,7-8H,4-6H2,1H3/b3-2+/t7-,8+,9-,10-/m0/s1
SMILES:  C[C@]1(/C=C/Cl)C[C@](CBr)([C@H](C[C@H]1Cl)Br)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL503864
PubChem CID:   6475605
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002867] Alkyl halides
        • [CHEMONTID:0004485] Cyclohexyl halides

*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
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. tenerife n.a. PMID[10924166]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[16309323]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[22220686]
NPO19226 Preussia africana Species Sporormiaceae Eukaryota n.a. n.a. n.a. PMID[22324636]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[24279991]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19226 Preussia africana Species Sporormiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18850 Aplysia dactylomela Species Aplysiidae 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
NPT1034 Cell Line Lu1 Homo sapiens IC50 = 12.9 ug.mL-1 PMID[536647]
NPT91 Cell Line KB Homo sapiens IC50 = 13.3 ug.mL-1 PMID[536647]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 = 7.8 ug.mL-1 PMID[536647]
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 2.0 mm PMID[536647]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 16.0 mm PMID[536647]
NPT1234 Organism Chlorella fusca Chlorella fusca MIC = 7.0 ug PMID[536647]
NPT176 Organism Artemia salina Artemia salina Activity = 100.0 % PMID[536647]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 32.0 ug.mL-1 PMID[536647]
NPT1513 Organism Mycobacterium avium Mycobacterium avium MIC = 34.0 ug.mL-1 PMID[536647]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi TIME = 1.0 hr PMID[536648]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi TIME = 0.8 hr PMID[536648]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 39.3 nmol/cm2 PMID[536648]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi TIME = 0.2 hr PMID[536648]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi EC50 = 1.2 nmol/cm2 PMID[536648]
NPT348 Organism Myzus persicae Myzus persicae EC50 = 1.0 nmol/cm2 PMID[536648]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi TIME = 0.001667 hr PMID[536648]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi TIME = 0.0 hr PMID[536648]

☑ 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 NPC183031 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
0.8065 Intermediate Similarity NPC52966
0.7667 Intermediate Similarity NPC469962
0.7407 Intermediate Similarity NPC99746
0.7344 Intermediate Similarity NPC110214
0.7097 Intermediate Similarity NPC469967
0.6909 Remote Similarity NPC160588
0.6909 Remote Similarity NPC180409
0.6557 Remote Similarity NPC469971
0.6545 Remote Similarity NPC51086
0.6316 Remote Similarity NPC474773
0.5645 Remote Similarity NPC159420

  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 NPC183031 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