Structure

Physi-Chem Properties

Molecular Weight:  238.01
Volume:  213.32
LogP:  4.247
LogD:  3.467
LogS:  -4.389
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.608
Synthetic Accessibility Score:  4.915
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:  -4.457
MDCK Permeability:  4.290607466828078e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.606
Plasma Protein Binding (PPB):  96.27318572998047%
Volume Distribution (VD):  2.321
Pgp-substrate:  4.430564880371094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.737
CYP1A2-substrate:  0.616
CYP2C19-inhibitor:  0.168
CYP2C19-substrate:  0.864
CYP2C9-inhibitor:  0.105
CYP2C9-substrate:  0.156
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.429
CYP3A4-inhibitor:  0.178
CYP3A4-substrate:  0.356

ADMET: Excretion

Clearance (CL):  6.652
Half-life (T1/2):  0.406

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.31
Drug-inuced Liver Injury (DILI):  0.108
AMES Toxicity:  0.289
Rat Oral Acute Toxicity:  0.398
Maximum Recommended Daily Dose:  0.946
Skin Sensitization:  0.641
Carcinogencity:  0.424
Eye Corrosion:  0.975
Eye Irritation:  0.979
Respiratory Toxicity:  0.974

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

  Natural Product: NPC159420

Natural Product ID:  NPC159420
Common Name*:   (3R,5S,6E)-3,5-Dichloro-6-(2-Chloroethylidene)-4,4-Dimethylcyclohexene
IUPAC Name:   (3R,5S,6E)-3,5-dichloro-6-(2-chloroethylidene)-4,4-dimethylcyclohexene
Synonyms:  
Standard InCHIKey:  HISRQLKATUAPCT-FQDVODHFSA-N
Standard InCHI:  InChI=1S/C10H13Cl3/c1-10(2)8(12)4-3-7(5-6-11)9(10)13/h3-5,8-9H,6H2,1-2H3/b7-5+/t8-,9+/m1/s1
SMILES:  CC1(C)[C@@H](C=C/C(=CCCl)/[C@@H]1Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL136637
PubChem CID:   14992544
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 = 20000.0 nM PMID[521852]
NPT3804 Cell Line Human Tumor Cell lines TGI = 47900.0 nM PMID[521852]
NPT3804 Cell Line Human Tumor Cell lines LC50 > 100000.0 nM PMID[521852]

☑ 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 NPC159420 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
0.7925 Intermediate Similarity NPC469967
0.7021 Intermediate Similarity NPC183670
0.6964 Remote Similarity NPC469962
0.6957 Remote Similarity NPC45727
0.6957 Remote Similarity NPC48638
0.6889 Remote Similarity NPC282119
0.6875 Remote Similarity NPC144023
0.68 Remote Similarity NPC473533
0.6735 Remote Similarity NPC177470
0.6604 Remote Similarity NPC17810
0.6596 Remote Similarity NPC239039
0.6531 Remote Similarity NPC469969
0.6531 Remote Similarity NPC259702
0.6383 Remote Similarity NPC34764
0.6383 Remote Similarity NPC190810
0.6383 Remote Similarity NPC76145
0.6383 Remote Similarity NPC201753
0.6364 Remote Similarity NPC469971
0.6364 Remote Similarity NPC66577
0.625 Remote Similarity NPC297643
0.625 Remote Similarity NPC139717
0.625 Remote Similarity NPC229262
0.6222 Remote Similarity NPC213749
0.62 Remote Similarity NPC218918
0.62 Remote Similarity NPC120926
0.6154 Remote Similarity NPC248411
0.614 Remote Similarity NPC37644
0.6136 Remote Similarity NPC60288
0.6122 Remote Similarity NPC55269
0.6038 Remote Similarity NPC114239
0.6038 Remote Similarity NPC86683
0.6038 Remote Similarity NPC13991
0.6038 Remote Similarity NPC296337
0.6038 Remote Similarity NPC241784
0.6 Remote Similarity NPC3649
0.6 Remote Similarity NPC206088
0.5962 Remote Similarity NPC99746
0.5932 Remote Similarity NPC470893
0.5918 Remote Similarity NPC266298
0.5909 Remote Similarity NPC138113
0.5882 Remote Similarity NPC107849
0.5862 Remote Similarity NPC295777
0.5862 Remote Similarity NPC69898
0.5862 Remote Similarity NPC476679
0.5833 Remote Similarity NPC249645
0.5833 Remote Similarity NPC55412
0.5833 Remote Similarity NPC92224
0.5818 Remote Similarity NPC124851
0.58 Remote Similarity NPC101811
0.5789 Remote Similarity NPC30433
0.5769 Remote Similarity NPC474773
0.5745 Remote Similarity NPC173592
0.5745 Remote Similarity NPC305759
0.5745 Remote Similarity NPC99088
0.5738 Remote Similarity NPC22019
0.5738 Remote Similarity NPC321568
0.5738 Remote Similarity NPC208749
0.5738 Remote Similarity NPC281986
0.5714 Remote Similarity NPC17518
0.5682 Remote Similarity NPC288991
0.5682 Remote Similarity NPC262789
0.5682 Remote Similarity NPC64176
0.566 Remote Similarity NPC109813
0.566 Remote Similarity NPC60556
0.566 Remote Similarity NPC86538
0.5645 Remote Similarity NPC469769
0.5645 Remote Similarity NPC183031
0.5636 Remote Similarity NPC323445
0.5625 Remote Similarity NPC200624

  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 NPC159420 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
0.6604 Remote Similarity NPD8262 Approved
0.6383 Remote Similarity NPD319 Phase 1
0.5833 Remote Similarity NPD4219 Approved

  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