Structure

Physi-Chem Properties

Molecular Weight:  414.0
Volume:  313.452
LogP:  5.858
LogD:  4.42
LogS:  -5.34
# 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:  4.726
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:  -4.541
MDCK Permeability:  1.8707451090449467e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.283
30% Bioavailability (F30%):  0.879

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.438
Plasma Protein Binding (PPB):  96.86518096923828%
Volume Distribution (VD):  1.318
Pgp-substrate:  5.213984966278076%

ADMET: Metabolism

CYP1A2-inhibitor:  0.717
CYP1A2-substrate:  0.879
CYP2C19-inhibitor:  0.684
CYP2C19-substrate:  0.934
CYP2C9-inhibitor:  0.919
CYP2C9-substrate:  0.169
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.404
CYP3A4-inhibitor:  0.631
CYP3A4-substrate:  0.905

ADMET: Excretion

Clearance (CL):  4.608
Half-life (T1/2):  0.12

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.634
Drug-inuced Liver Injury (DILI):  0.786
AMES Toxicity:  0.131
Rat Oral Acute Toxicity:  0.401
Maximum Recommended Daily Dose:  0.345
Skin Sensitization:  0.883
Carcinogencity:  0.671
Eye Corrosion:  0.985
Eye Irritation:  0.823
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC308569

Natural Product ID:  NPC308569
Common Name*:   Caespitane
IUPAC Name:   (3R,6S)-3-bromo-6-[(1S,3S,4S)-3-bromo-4-chloro-4-methylcyclohexyl]-2,2,6-trimethyloxane
Synonyms:   Caespitane
Standard InCHIKey:  FIHHUYBIKUKVFD-XXUMUBMXSA-N
Standard InCHI:  InChI=1S/C15H25Br2ClO/c1-13(2)11(16)6-8-15(4,19-13)10-5-7-14(3,18)12(17)9-10/h10-12H,5-9H2,1-4H3/t10-,11+,12-,14-,15-/m0/s1
SMILES:  CC1(C)[C@@H](CC[C@@](C)([C@H]2CC[C@@](C)([C@H](C2)Br)Cl)O1)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL497523
PubChem CID:   14314411
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]
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]
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 > 25.0 ug.mL-1 PMID[464761]
NPT91 Cell Line KB Homo sapiens IC50 > 25.0 ug.mL-1 PMID[464761]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[464761]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 1.0 mm PMID[464761]
NPT176 Organism Artemia salina Artemia salina Activity = 40.0 % PMID[464761]

☑ 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 NPC308569 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
1.0 High Similarity NPC469572
1.0 High Similarity NPC469582
0.8667 High Similarity NPC469573
0.8209 Intermediate Similarity NPC83368
0.8088 Intermediate Similarity NPC33876
0.8088 Intermediate Similarity NPC277993
0.7879 Intermediate Similarity NPC475786
0.7857 Intermediate Similarity NPC469581
0.7432 Intermediate Similarity NPC469580
0.7222 Intermediate Similarity NPC150938
0.7051 Intermediate Similarity NPC469556
0.6962 Remote Similarity NPC469555
0.6892 Remote Similarity NPC30575
0.6667 Remote Similarity NPC302939
0.6667 Remote Similarity NPC287331
0.641 Remote Similarity NPC83436
0.6092 Remote Similarity NPC469538
0.5946 Remote Similarity NPC301725
0.593 Remote Similarity NPC76909
0.5904 Remote Similarity NPC97491
0.5904 Remote Similarity NPC273356
0.5833 Remote Similarity NPC282598
0.5824 Remote Similarity NPC475934
0.5802 Remote Similarity NPC31330
0.5802 Remote Similarity NPC476603
0.5769 Remote Similarity NPC237510
0.5769 Remote Similarity NPC475793
0.5765 Remote Similarity NPC48210
0.5765 Remote Similarity NPC469570
0.5667 Remote Similarity NPC82843
0.5658 Remote Similarity NPC476604
0.5645 Remote Similarity NPC108441
0.5645 Remote Similarity NPC77550
0.5632 Remote Similarity NPC280810

  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 NPC308569 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
0.6667 Remote Similarity NPD367 Approved
0.5645 Remote Similarity NPD386 Approved
0.5645 Remote Similarity NPD388 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