Structure

Physi-Chem Properties

Molecular Weight:  248.01
Volume:  246.266
LogP:  4.304
LogD:  2.503
LogS:  -5.141
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.596
Synthetic Accessibility Score:  4.359
Fsp3:  0.231
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:  -4.161
MDCK Permeability:  1.8167513189837337e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.084
20% Bioavailability (F20%):  0.851
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  101.9393310546875%
Volume Distribution (VD):  1.798
Pgp-substrate:  2.1039884090423584%

ADMET: Metabolism

CYP1A2-inhibitor:  0.974
CYP1A2-substrate:  0.686
CYP2C19-inhibitor:  0.881
CYP2C19-substrate:  0.423
CYP2C9-inhibitor:  0.916
CYP2C9-substrate:  0.921
CYP2D6-inhibitor:  0.164
CYP2D6-substrate:  0.586
CYP3A4-inhibitor:  0.79
CYP3A4-substrate:  0.255

ADMET: Excretion

Clearance (CL):  8.862
Half-life (T1/2):  0.05

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.642
Drug-inuced Liver Injury (DILI):  0.979
AMES Toxicity:  0.856
Rat Oral Acute Toxicity:  0.986
Maximum Recommended Daily Dose:  0.995
Skin Sensitization:  0.946
Carcinogencity:  0.474
Eye Corrosion:  0.978
Eye Irritation:  0.989
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: NPC67485

Natural Product ID:  NPC67485
Common Name*:   YSYBCKHAFOAQDX-NSHDSACASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YSYBCKHAFOAQDX-NSHDSACASA-N
Standard InCHI:  InChI=1S/C13H9ClOS/c1-2-3-4-5-12-8-9-13(16-12)7-6-11(15)10-14/h8-9,11,15H,10H2,1H3/t11-/m0/s1
SMILES:  CC#CC#Cc1ccc(C#C[C@@H](CCl)O)s1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   86310851
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000097] Thiophenes
        • [CHEMONTID:0003481] 2,5-disubstituted thiophenes

*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
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[12608846]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[17880175]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20648 Streptomyces cellulosae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19410 Clutia abyssinica Species Peraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20718 Hypericum elegans Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9531 Premna latifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20431 Centaurea canariensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19837 Euonymus latifolius Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17115 Kielmeyera petiolaris Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20101 Eria acutifolia Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17908 Rhododendron reticulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20233 Marchantia paleacea Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26309 Ahnfeltiopsis flabelliformis Species Phyllophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20982 Morus lactea Species Sulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19559 Cetraria pseudocomplicata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14172 Rhopaloeides odorabile Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3468 Astragalus floccosifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18749 Corydalis vernyi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11034 Mnium pseudopunctatum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4687 Gyromitra esculenta Species Discinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21251 Tabernaemontana odoratissima Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19272 Alcyonium fauri Species Alcyoniidae 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

☑ 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 NPC67485 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

  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 NPC67485 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

  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