Structure

Physi-Chem Properties

Molecular Weight:  172.03
Volume:  190.31
LogP:  4.057
LogD:  3.065
LogS:  -4.496
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.528
Synthetic Accessibility Score:  3.64
Fsp3:  0.091
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.709
MDCK Permeability:  9.65098079177551e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.029
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  100.29431915283203%
Volume Distribution (VD):  1.863
Pgp-substrate:  1.5797734260559082%

ADMET: Metabolism

CYP1A2-inhibitor:  0.987
CYP1A2-substrate:  0.88
CYP2C19-inhibitor:  0.955
CYP2C19-substrate:  0.603
CYP2C9-inhibitor:  0.933
CYP2C9-substrate:  0.972
CYP2D6-inhibitor:  0.868
CYP2D6-substrate:  0.898
CYP3A4-inhibitor:  0.874
CYP3A4-substrate:  0.512

ADMET: Excretion

Clearance (CL):  4.108
Half-life (T1/2):  0.085

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.808
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.81
Rat Oral Acute Toxicity:  0.028
Maximum Recommended Daily Dose:  0.352
Skin Sensitization:  0.946
Carcinogencity:  0.648
Eye Corrosion:  0.987
Eye Irritation:  0.995
Respiratory Toxicity:  0.894

Download Data

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

  Natural Product: NPC105991

Natural Product ID:  NPC105991
Common Name*:   Xanthopappin A
IUPAC Name:   2-[(E)-hept-5-en-1,3-diynyl]thiophene
Synonyms:  
Standard InCHIKey:  VDPJXBAVKXXKLA-NSCUHMNNSA-N
Standard InCHI:  InChI=1S/C11H8S/c1-2-3-4-5-6-8-11-9-7-10-12-11/h2-3,7,9-10H,1H3/b3-2+
SMILES:  C/C=C/C#CC#Cc1cccs1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453761
PubChem CID:   16083186
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004144] Heteroaromatic compounds

*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 = 0.71 ug.mL-1 PMID[458471]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 > 10.0 ug.mL-1 PMID[458471]

☑ 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 NPC105991 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
0.8649 High Similarity NPC8981
0.8267 Intermediate Similarity NPC299367
0.7945 Intermediate Similarity NPC470796
0.7821 Intermediate Similarity NPC195713
0.775 Intermediate Similarity NPC472169
0.7412 Intermediate Similarity NPC2751
0.7333 Intermediate Similarity NPC470795
0.7317 Intermediate Similarity NPC307163
0.7284 Intermediate Similarity NPC471376
0.7222 Intermediate Similarity NPC22627
0.7126 Intermediate Similarity NPC166487
0.7108 Intermediate Similarity NPC471895
0.7077 Intermediate Similarity NPC108375
0.6912 Remote Similarity NPC476214
0.6889 Remote Similarity NPC300455
0.686 Remote Similarity NPC148231
0.6848 Remote Similarity NPC474934
0.6761 Remote Similarity NPC469807
0.6739 Remote Similarity NPC175376
0.6628 Remote Similarity NPC470794
0.6562 Remote Similarity NPC475115
0.6421 Remote Similarity NPC120203
0.6392 Remote Similarity NPC472171
0.6329 Remote Similarity NPC5324
0.6327 Remote Similarity NPC472172
0.63 Remote Similarity NPC475086
0.6289 Remote Similarity NPC11466
0.6263 Remote Similarity NPC472170
0.6224 Remote Similarity NPC24122
0.6224 Remote Similarity NPC173019
0.6076 Remote Similarity NPC52330
0.6022 Remote Similarity NPC470797
0.5962 Remote Similarity NPC190955
0.593 Remote Similarity NPC67863
0.5921 Remote Similarity NPC169110
0.5844 Remote Similarity NPC45255
0.5833 Remote Similarity NPC32356
0.5778 Remote Similarity NPC125549
0.575 Remote Similarity NPC36440
0.5714 Remote Similarity NPC212463
0.5688 Remote Similarity NPC221877
0.5652 Remote Similarity NPC11150

  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 NPC105991 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
0.6739 Remote Similarity NPD532 Approved
0.6667 Remote Similarity NPD1672 Phase 2
0.6327 Remote Similarity NPD793 Approved
0.62 Remote Similarity NPD745 Clinical (unspecified phase)
0.6139 Remote Similarity NPD3459 Approved
0.6139 Remote Similarity NPD183 Approved
0.6019 Remote Similarity NPD2242 Phase 1
0.5962 Remote Similarity NPD5278 Discontinued
0.5922 Remote Similarity NPD445 Discontinued
0.5851 Remote Similarity NPD4728 Approved
0.581 Remote Similarity NPD2298 Clinical (unspecified phase)
0.5794 Remote Similarity NPD1279 Clinical (unspecified phase)
0.578 Remote Similarity NPD1944 Phase 2
0.5741 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5741 Remote Similarity NPD2587 Approved
0.5684 Remote Similarity NPD2811 Clinical (unspecified phase)
0.5648 Remote Similarity NPD1265 Approved
0.5648 Remote Similarity NPD1267 Approved
0.5604 Remote Similarity NPD9303 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