Structure

Physi-Chem Properties

Molecular Weight:  263.17
Volume:  283.856
LogP:  5.738
LogD:  5.332
LogS:  -5.315
# Rotatable Bonds:  2
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.525
Synthetic Accessibility Score:  5.453
Fsp3:  0.938
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.714
MDCK Permeability:  2.9149145120754838e-05
Pgp-inhibitor:  0.242
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.083
30% Bioavailability (F30%):  0.167

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.957
Plasma Protein Binding (PPB):  32.719478607177734%
Volume Distribution (VD):  1.315
Pgp-substrate:  39.543357849121094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.151
CYP1A2-substrate:  0.228
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.936
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.395
CYP2D6-substrate:  0.346
CYP3A4-inhibitor:  0.485
CYP3A4-substrate:  0.514

ADMET: Excretion

Clearance (CL):  9.861
Half-life (T1/2):  0.108

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.145
Drug-inuced Liver Injury (DILI):  0.834
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.954
Maximum Recommended Daily Dose:  0.129
Skin Sensitization:  0.75
Carcinogencity:  0.548
Eye Corrosion:  0.986
Eye Irritation:  0.614
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC475272

Natural Product ID:  NPC475272
Common Name*:   PFDINSDEWOBSRZ-HFVXDEDMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PFDINSDEWOBSRZ-HFVXDEDMSA-N
Standard InCHI:  InChI=1S/C16H25NS/c1-10-7-8-16-11(2)5-6-12(14(16)13(10)16)15(3,4)17-9-18/h10-14H,5-8H2,1-4H3/t10-,11-,12-,13+,14+,16-/m0/s1
SMILES:  S=C=NC([C@H]1CC[C@@H]([C@]23[C@H]1[C@H]2[C@@H](C)CC3)C)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL502488
PubChem CID:   11334543
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO33096 stylissa sp. Species Axinellidae Eukaryota n.a. Okinawan n.a. PMID[15165146]

☑ 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 57800.0 nM PMID[466402]

☑ 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 NPC475272 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
0.7593 Intermediate Similarity NPC472829
0.7193 Intermediate Similarity NPC472828
0.7097 Intermediate Similarity NPC477739
0.7049 Intermediate Similarity NPC152211
0.7049 Intermediate Similarity NPC28755
0.6852 Remote Similarity NPC181141
0.6719 Remote Similarity NPC477740
0.6719 Remote Similarity NPC475755
0.6667 Remote Similarity NPC311809
0.6508 Remote Similarity NPC21781
0.6418 Remote Similarity NPC474456
0.6418 Remote Similarity NPC37792
0.6232 Remote Similarity NPC271640
0.623 Remote Similarity NPC476676
0.6212 Remote Similarity NPC145715
0.6143 Remote Similarity NPC124384
0.6143 Remote Similarity NPC184919
0.6143 Remote Similarity NPC245223
0.6119 Remote Similarity NPC473959
0.6119 Remote Similarity NPC53276
0.6029 Remote Similarity NPC469970
0.597 Remote Similarity NPC474435
0.597 Remote Similarity NPC474027
0.5902 Remote Similarity NPC212905
0.5833 Remote Similarity NPC201713
0.5758 Remote Similarity NPC472827
0.5652 Remote Similarity NPC476682
0.5616 Remote Similarity NPC473442
0.5616 Remote Similarity NPC120167

  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 NPC475272 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
0.6032 Remote Similarity NPD628 Phase 3
0.6032 Remote Similarity NPD627 Approved
0.6032 Remote Similarity NPD625 Approved
0.6032 Remote Similarity NPD626 Phase 3
0.5849 Remote Similarity NPD636 Phase 3
0.5849 Remote Similarity NPD635 Phase 3
0.5833 Remote Similarity NPD4834 Discontinued
0.5789 Remote Similarity NPD873 Approved
0.5789 Remote Similarity NPD871 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