Structure

Physi-Chem Properties

Molecular Weight:  346.03
Volume:  295.049
LogP:  4.196
LogD:  3.94
LogS:  -4.499
# Rotatable Bonds:  3
TPSA:  18.46
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.573
Synthetic Accessibility Score:  5.919
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.335
MDCK Permeability:  3.142797140753828e-05
Pgp-inhibitor:  0.406
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.299

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.163
Plasma Protein Binding (PPB):  92.65135192871094%
Volume Distribution (VD):  2.335
Pgp-substrate:  2.9501161575317383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.216
CYP1A2-substrate:  0.797
CYP2C19-inhibitor:  0.813
CYP2C19-substrate:  0.87
CYP2C9-inhibitor:  0.828
CYP2C9-substrate:  0.03
CYP2D6-inhibitor:  0.022
CYP2D6-substrate:  0.176
CYP3A4-inhibitor:  0.921
CYP3A4-substrate:  0.603

ADMET: Excretion

Clearance (CL):  10.843
Half-life (T1/2):  0.252

ADMET: Toxicity

hERG Blockers:  0.167
Human Hepatotoxicity (H-HT):  0.188
Drug-inuced Liver Injury (DILI):  0.921
AMES Toxicity:  0.168
Rat Oral Acute Toxicity:  0.507
Maximum Recommended Daily Dose:  0.821
Skin Sensitization:  0.951
Carcinogencity:  0.766
Eye Corrosion:  0.977
Eye Irritation:  0.99
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: NPC52781

Natural Product ID:  NPC52781
Common Name*:   3(Z)-Chlorofucin
IUPAC Name:   (1S,2S,4S,5R,7S,8S)-4-bromo-2-chloro-5-ethyl-8-[(Z)-pent-2-en-4-ynyl]-6,9-dioxabicyclo[5.2.1]decane
Synonyms:   3(Z)-Chlorofucin
Standard InCHIKey:  VRGYZGMXCGNRKB-DFGSKXRTSA-N
Standard InCHI:  InChI=1S/C15H20BrClO2/c1-3-5-6-7-13-15-9-14(19-13)11(17)8-10(16)12(4-2)18-15/h1,5-6,10-15H,4,7-9H2,2H3/b6-5-/t10-,11-,12+,13-,14-,15-/m0/s1
SMILES:  C#C/C=CC[C@@H]1O[C@H]2C[C@@H]1O[C@H](CC)[C@H](C[C@@H]2Cl)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL477735
PubChem CID:   11100112
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002648] Tetrahydrofurans

*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
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. Malaysian n.a. PMID[11374951]
NPO27012 Laurencia pannosa 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
NPT2631 Organism Chromobacterium violaceum Chromobacterium violaceum MIC = 100.0 ug PMID[570238]

☑ 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 NPC52781 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
0.8243 Intermediate Similarity NPC473306
0.8108 Intermediate Similarity NPC477423
0.7867 Intermediate Similarity NPC473453
0.7838 Intermediate Similarity NPC477431
0.7632 Intermediate Similarity NPC325098
0.7342 Intermediate Similarity NPC477422
0.7326 Intermediate Similarity NPC477428
0.725 Intermediate Similarity NPC477421
0.7067 Intermediate Similarity NPC271000
0.6892 Remote Similarity NPC477430
0.6835 Remote Similarity NPC316572
0.675 Remote Similarity NPC323677
0.675 Remote Similarity NPC477429
0.65 Remote Similarity NPC471472
0.6486 Remote Similarity NPC26310
0.6234 Remote Similarity NPC477424
0.6154 Remote Similarity NPC30915
0.6136 Remote Similarity NPC473947
0.6098 Remote Similarity NPC473294
0.6 Remote Similarity NPC471460
0.5851 Remote Similarity NPC247826
0.5769 Remote Similarity NPC23418
0.5684 Remote Similarity NPC184461
0.5625 Remote Similarity NPC226872
0.5625 Remote Similarity NPC158368
0.5625 Remote Similarity NPC154908
0.5625 Remote Similarity NPC252851
0.5625 Remote Similarity NPC475405

  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 NPC52781 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