Structure

Physi-Chem Properties

Molecular Weight:  250.02
Volume:  248.903
LogP:  3.67
LogD:  2.037
LogS:  -4.078
# Rotatable Bonds:  2
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.632
Synthetic Accessibility Score:  4.261
Fsp3:  0.231
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.842
MDCK Permeability:  1.4222971913113724e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.181
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.85

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  100.86587524414062%
Volume Distribution (VD):  1.669
Pgp-substrate:  1.5852527618408203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.969
CYP1A2-substrate:  0.869
CYP2C19-inhibitor:  0.949
CYP2C19-substrate:  0.648
CYP2C9-inhibitor:  0.937
CYP2C9-substrate:  0.98
CYP2D6-inhibitor:  0.841
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.852
CYP3A4-substrate:  0.624

ADMET: Excretion

Clearance (CL):  3.806
Half-life (T1/2):  0.069

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.745
Drug-inuced Liver Injury (DILI):  0.975
AMES Toxicity:  0.731
Rat Oral Acute Toxicity:  0.856
Maximum Recommended Daily Dose:  0.849
Skin Sensitization:  0.889
Carcinogencity:  0.83
Eye Corrosion:  0.396
Eye Irritation:  0.927
Respiratory Toxicity:  0.891

Download Data

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

  Natural Product: NPC475115

Natural Product ID:  NPC475115
Common Name*:   Xanthopappin B
IUPAC Name:   2-chloro-1-[5-[(E)-hept-5-en-1,3-diynyl]thiophen-2-yl]ethanol
Synonyms:   xanthopappin B
Standard InCHIKey:  MMMJOLFAYHLDBI-NSCUHMNNSA-N
Standard InCHI:  InChI=1S/C13H11ClOS/c1-2-3-4-5-6-7-11-8-9-13(16-11)12(15)10-14/h2-3,8-9,12,15H,10H2,1H3/b3-2+
SMILES:  C/C=C/C#CC#Cc1ccc(s1)C(CCl)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL498465
PubChem CID:   16083187
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
NPO24814 Xanthopappus subacaulis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16933888]
NPO24814 Xanthopappus subacaulis Species Asteraceae 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
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 = 0.53 ug.mL-1 PMID[520667]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 = 5.1 ug.mL-1 PMID[520667]

☑ 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 NPC475115 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
0.883 High Similarity NPC2751
0.8776 High Similarity NPC474934
0.8095 Intermediate Similarity NPC472170
0.766 Intermediate Similarity NPC299367
0.7629 Intermediate Similarity NPC472169
0.7407 Intermediate Similarity NPC173019
0.7297 Intermediate Similarity NPC475086
0.6786 Remote Similarity NPC472171
0.6726 Remote Similarity NPC472172
0.6562 Remote Similarity NPC105991
0.6529 Remote Similarity NPC32356
0.6357 Remote Similarity NPC475082
0.6214 Remote Similarity NPC8981
0.619 Remote Similarity NPC87299
0.619 Remote Similarity NPC329319
0.619 Remote Similarity NPC99394
0.619 Remote Similarity NPC103326
0.6182 Remote Similarity NPC166487
0.6129 Remote Similarity NPC221877
0.6095 Remote Similarity NPC117180
0.6075 Remote Similarity NPC304538
0.6018 Remote Similarity NPC300455
0.5865 Remote Similarity NPC66655
0.5833 Remote Similarity NPC172984
0.5833 Remote Similarity NPC307163
0.578 Remote Similarity NPC470794
0.5726 Remote Similarity NPC190955
0.5701 Remote Similarity NPC195713
0.5688 Remote Similarity NPC471895
0.5676 Remote Similarity NPC93843
0.5664 Remote Similarity NPC1793
0.5656 Remote Similarity NPC472919
0.5648 Remote Similarity NPC133050
0.5641 Remote Similarity NPC175376
0.563 Remote Similarity NPC275104
0.5625 Remote Similarity NPC211237
0.5603 Remote Similarity NPC138117
0.5603 Remote Similarity NPC325292

  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 NPC475115 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
0.64 Remote Similarity NPD446 Clinical (unspecified phase)
0.609 Remote Similarity NPD767 Phase 1
0.6077 Remote Similarity NPD1877 Discontinued
0.6058 Remote Similarity NPD2202 Clinical (unspecified phase)
0.5912 Remote Similarity NPD4404 Approved
0.5873 Remote Similarity NPD1246 Approved
0.5873 Remote Similarity NPD911 Approved
0.5865 Remote Similarity NPD9294 Approved
0.5857 Remote Similarity NPD5886 Approved
0.5857 Remote Similarity NPD41 Approved
0.5852 Remote Similarity NPD2035 Discontinued
0.584 Remote Similarity NPD1105 Clinical (unspecified phase)
0.5794 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5775 Remote Similarity NPD7137 Phase 2
0.5726 Remote Similarity NPD5278 Discontinued
0.5714 Remote Similarity NPD4273 Approved
0.5694 Remote Similarity NPD2447 Discontinued
0.5652 Remote Similarity NPD9251 Approved
0.5649 Remote Similarity NPD1245 Approved
0.56 Remote Similarity NPD910 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