Structure

Physi-Chem Properties

Molecular Weight:  414.0
Volume:  313.452
LogP:  5.746
LogD:  4.396
LogS:  -5.485
# Rotatable Bonds:  1
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.501
Synthetic Accessibility Score:  4.875
Fsp3:  1.0
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:  -4.532
MDCK Permeability:  1.6828618754516356e-05
Pgp-inhibitor:  0.752
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.05
30% Bioavailability (F30%):  0.356

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.554
Plasma Protein Binding (PPB):  98.47163391113281%
Volume Distribution (VD):  1.647
Pgp-substrate:  3.526984453201294%

ADMET: Metabolism

CYP1A2-inhibitor:  0.375
CYP1A2-substrate:  0.686
CYP2C19-inhibitor:  0.546
CYP2C19-substrate:  0.939
CYP2C9-inhibitor:  0.895
CYP2C9-substrate:  0.537
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.845
CYP3A4-inhibitor:  0.492
CYP3A4-substrate:  0.628

ADMET: Excretion

Clearance (CL):  3.671
Half-life (T1/2):  0.148

ADMET: Toxicity

hERG Blockers:  0.076
Human Hepatotoxicity (H-HT):  0.446
Drug-inuced Liver Injury (DILI):  0.807
AMES Toxicity:  0.097
Rat Oral Acute Toxicity:  0.116
Maximum Recommended Daily Dose:  0.141
Skin Sensitization:  0.646
Carcinogencity:  0.412
Eye Corrosion:  0.99
Eye Irritation:  0.928
Respiratory Toxicity:  0.964

Download Data

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

  Natural Product: NPC469573

Natural Product ID:  NPC469573
Common Name*:   Deoxy Isocaespitol
IUPAC Name:   (3S,6R)-3-bromo-6-[(1R,3S,4S)-4-bromo-3-chloro-4-methylcyclohexyl]-2,2,6-trimethyloxane
Synonyms:   Deoxy Isocaespitol
Standard InCHIKey:  FGWVVJIZZSRMKT-FUQNVFFISA-N
Standard InCHI:  InChI=1S/C15H25Br2ClO/c1-13(2)11(16)6-8-15(4,19-13)10-5-7-14(3,17)12(18)9-10/h10-12H,5-9H2,1-4H3/t10-,11+,12+,14+,15-/m1/s1
SMILES:  Br[C@H]1CC[C@](OC1(C)C)(C)[C@@H]1CC[C@]([C@H](C1)Cl)(C)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1088007
PubChem CID:   46881071
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
NPO29486 Laurencia catarinensis Species Rhodomelaceae Eukaryota n.a. Brazilian n.a. PMID[20039643]
NPO29486 Laurencia catarinensis Species Rhodomelaceae 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
NPT139 Cell Line HT-29 Homo sapiens IC50 = 27300.0 nM PMID[518895]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 31700.0 nM PMID[518895]
NPT762 Cell Line A-431 Homo sapiens IC50 = 30700.0 nM PMID[518895]

☑ 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 NPC469573 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
0.8667 High Similarity NPC469572
0.8667 High Similarity NPC308569
0.8667 High Similarity NPC469582
0.8261 Intermediate Similarity NPC150938
0.7222 Intermediate Similarity NPC83368
0.7123 Intermediate Similarity NPC277993
0.7123 Intermediate Similarity NPC33876
0.6933 Remote Similarity NPC469581
0.6901 Remote Similarity NPC475786
0.6582 Remote Similarity NPC469580
0.6441 Remote Similarity NPC302939
0.6441 Remote Similarity NPC287331
0.6353 Remote Similarity NPC76909
0.6341 Remote Similarity NPC97491
0.6341 Remote Similarity NPC273356
0.6265 Remote Similarity NPC469556
0.619 Remote Similarity NPC469555
0.6076 Remote Similarity NPC30575
0.6056 Remote Similarity NPC110214
0.5789 Remote Similarity NPC301725
0.5663 Remote Similarity NPC83436
0.5647 Remote Similarity NPC215175

  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 NPC469573 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
0.6441 Remote Similarity NPD367 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