Structure

Physi-Chem Properties

Molecular Weight:  456.09
Volume:  479.641
LogP:  5.531
LogD:  3.491
LogS:  -5.486
# Rotatable Bonds:  5
TPSA:  54.37
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.523
Synthetic Accessibility Score:  4.742
Fsp3:  0.185
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.013
MDCK Permeability:  1.196638277178863e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.921
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.128

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  105.4914779663086%
Volume Distribution (VD):  1.939
Pgp-substrate:  1.3276230096817017%

ADMET: Metabolism

CYP1A2-inhibitor:  0.667
CYP1A2-substrate:  0.81
CYP2C19-inhibitor:  0.852
CYP2C19-substrate:  0.493
CYP2C9-inhibitor:  0.858
CYP2C9-substrate:  0.994
CYP2D6-inhibitor:  0.594
CYP2D6-substrate:  0.889
CYP3A4-inhibitor:  0.888
CYP3A4-substrate:  0.912

ADMET: Excretion

Clearance (CL):  1.342
Half-life (T1/2):  0.003

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.977
Drug-inuced Liver Injury (DILI):  0.994
AMES Toxicity:  0.695
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.256
Skin Sensitization:  0.958
Carcinogencity:  0.716
Eye Corrosion:  0.024
Eye Irritation:  0.308
Respiratory Toxicity:  0.056

Download Data

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

  Natural Product: NPC475082

Natural Product ID:  NPC475082
Common Name*:   Xanthopappin C
IUPAC Name:   1,2-bis[5-[(E)-hept-5-en-1,3-diynyl]thiophen-2-yl]-2-hydroxypentane-1,4-dione
Synonyms:   xanthopappin C
Standard InCHIKey:  YIPZRWXKZQNUSS-YDFGWWAZSA-N
Standard InCHI:  InChI=1S/C27H20O3S2/c1-4-6-8-10-12-14-22-16-18-24(31-22)26(29)27(30,20-21(3)28)25-19-17-23(32-25)15-13-11-9-7-5-2/h4-7,16-19,30H,20H2,1-3H3/b6-4+,7-5+
SMILES:  CC=CC#CC#CC1=CC=C(S1)C(=O)C(CC(=O)C)(C2=CC=C(S2)C#CC#CC=CC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL496243
PubChem CID:   16083190
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0003671] Aryl alkyl ketones

*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 = 0.95 ug.mL-1 PMID[471303]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 > 10.0 ug.mL-1 PMID[471303]

☑ 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 NPC475082 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
0.7177 Intermediate Similarity NPC472170
0.7167 Intermediate Similarity NPC175376
0.7154 Intermediate Similarity NPC32356
0.6829 Remote Similarity NPC474934
0.671 Remote Similarity NPC85059
0.6667 Remote Similarity NPC2751
0.6641 Remote Similarity NPC249067
0.6614 Remote Similarity NPC173019
0.6484 Remote Similarity NPC24122
0.6484 Remote Similarity NPC25458
0.6412 Remote Similarity NPC475086
0.6357 Remote Similarity NPC475115
0.6343 Remote Similarity NPC476003
0.6343 Remote Similarity NPC474057
0.6341 Remote Similarity NPC145990
0.6328 Remote Similarity NPC217621
0.6316 Remote Similarity NPC224584
0.6303 Remote Similarity NPC307163
0.6277 Remote Similarity NPC93181
0.6269 Remote Similarity NPC95172
0.625 Remote Similarity NPC229242
0.6241 Remote Similarity NPC249811
0.6231 Remote Similarity NPC472171
0.6231 Remote Similarity NPC304873
0.6214 Remote Similarity NPC249435
0.6212 Remote Similarity NPC105899
0.6187 Remote Similarity NPC477453
0.6183 Remote Similarity NPC255676
0.6183 Remote Similarity NPC274443
0.6183 Remote Similarity NPC472172
0.6181 Remote Similarity NPC118853
0.6176 Remote Similarity NPC268388
0.6176 Remote Similarity NPC292834
0.6172 Remote Similarity NPC253423
0.6172 Remote Similarity NPC289201
0.617 Remote Similarity NPC472708
0.6164 Remote Similarity NPC474106
0.616 Remote Similarity NPC110704
0.6159 Remote Similarity NPC274839
0.6143 Remote Similarity NPC121259
0.6143 Remote Similarity NPC269414
0.6119 Remote Similarity NPC226699
0.6119 Remote Similarity NPC141523
0.6119 Remote Similarity NPC34715
0.6116 Remote Similarity NPC470794
0.6115 Remote Similarity NPC322197
0.6115 Remote Similarity NPC161304
0.6115 Remote Similarity NPC23402
0.6107 Remote Similarity NPC244427
0.6107 Remote Similarity NPC222390
0.6103 Remote Similarity NPC116842
0.609 Remote Similarity NPC172483
0.6087 Remote Similarity NPC196673
0.6087 Remote Similarity NPC242136
0.6087 Remote Similarity NPC11824
0.608 Remote Similarity NPC62765
0.6077 Remote Similarity NPC325497
0.6069 Remote Similarity NPC472704
0.6069 Remote Similarity NPC477153
0.6061 Remote Similarity NPC329556
0.6058 Remote Similarity NPC212718
0.6058 Remote Similarity NPC66208
0.6058 Remote Similarity NPC114682
0.6056 Remote Similarity NPC195262
0.6056 Remote Similarity NPC188814
0.6047 Remote Similarity NPC156021
0.6045 Remote Similarity NPC100767
0.6045 Remote Similarity NPC29989
0.6045 Remote Similarity NPC6984
0.6045 Remote Similarity NPC69332
0.6045 Remote Similarity NPC95178
0.6043 Remote Similarity NPC285350
0.6043 Remote Similarity NPC186933
0.6031 Remote Similarity NPC282895
0.6029 Remote Similarity NPC88141
0.6027 Remote Similarity NPC295664
0.6016 Remote Similarity NPC206764
0.6014 Remote Similarity NPC472707
0.6 Remote Similarity NPC65627
0.6 Remote Similarity NPC472703
0.6 Remote Similarity NPC240163
0.6 Remote Similarity NPC211439
0.6 Remote Similarity NPC11821
0.6 Remote Similarity NPC68167
0.5987 Remote Similarity NPC106247
0.5986 Remote Similarity NPC41567
0.5985 Remote Similarity NPC320891
0.5985 Remote Similarity NPC21162
0.5985 Remote Similarity NPC284477
0.5973 Remote Similarity NPC21305
0.5972 Remote Similarity NPC472981
0.5971 Remote Similarity NPC153053
0.5971 Remote Similarity NPC211421
0.5971 Remote Similarity NPC474363
0.597 Remote Similarity NPC134120
0.5969 Remote Similarity NPC61944
0.5957 Remote Similarity NPC474987
0.5957 Remote Similarity NPC76844
0.5957 Remote Similarity NPC158157
0.5956 Remote Similarity NPC317305
0.5956 Remote Similarity NPC318327
0.5956 Remote Similarity NPC17525
0.5956 Remote Similarity NPC85493
0.5954 Remote Similarity NPC228435
0.5948 Remote Similarity NPC159786
0.5946 Remote Similarity NPC473751
0.5946 Remote Similarity NPC306765
0.5946 Remote Similarity NPC62952
0.5946 Remote Similarity NPC231774
0.5946 Remote Similarity NPC81135
0.5944 Remote Similarity NPC204784
0.5942 Remote Similarity NPC321852
0.594 Remote Similarity NPC247976
0.594 Remote Similarity NPC301943
0.594 Remote Similarity NPC474365
0.5938 Remote Similarity NPC34243
0.5935 Remote Similarity NPC477534
0.5933 Remote Similarity NPC474998
0.5931 Remote Similarity NPC303737
0.5931 Remote Similarity NPC196976
0.5931 Remote Similarity NPC167323
0.5931 Remote Similarity NPC269923
0.5931 Remote Similarity NPC18785
0.5929 Remote Similarity NPC276111
0.5929 Remote Similarity NPC469509
0.5929 Remote Similarity NPC118288
0.5929 Remote Similarity NPC476357
0.5926 Remote Similarity NPC70843
0.5918 Remote Similarity NPC310540
0.5918 Remote Similarity NPC142956
0.5906 Remote Similarity NPC100067
0.5906 Remote Similarity NPC23126
0.5906 Remote Similarity NPC169250
0.5906 Remote Similarity NPC105157
0.5906 Remote Similarity NPC30501
0.5906 Remote Similarity NPC266689
0.5906 Remote Similarity NPC103356
0.5906 Remote Similarity NPC162612
0.5906 Remote Similarity NPC72158
0.5906 Remote Similarity NPC98254
0.5906 Remote Similarity NPC190043
0.5903 Remote Similarity NPC285829
0.5903 Remote Similarity NPC206778
0.5903 Remote Similarity NPC232958
0.5903 Remote Similarity NPC133302
0.5899 Remote Similarity NPC143768
0.5897 Remote Similarity NPC107571
0.5896 Remote Similarity NPC8931
0.5896 Remote Similarity NPC120693
0.5896 Remote Similarity NPC261573
0.5896 Remote Similarity NPC329282
0.589 Remote Similarity NPC309765
0.589 Remote Similarity NPC307174
0.589 Remote Similarity NPC300274
0.589 Remote Similarity NPC139171
0.5887 Remote Similarity NPC28054
0.5878 Remote Similarity NPC160548
0.5878 Remote Similarity NPC236405
0.5878 Remote Similarity NPC210529
0.5878 Remote Similarity NPC79608
0.5878 Remote Similarity NPC287473
0.5878 Remote Similarity NPC175852
0.5874 Remote Similarity NPC161943
0.5874 Remote Similarity NPC254958
0.5874 Remote Similarity NPC474890
0.5874 Remote Similarity NPC318173
0.5874 Remote Similarity NPC184527
0.5874 Remote Similarity NPC273282
0.5874 Remote Similarity NPC291619
0.5871 Remote Similarity NPC473268
0.587 Remote Similarity NPC321252
0.587 Remote Similarity NPC260818
0.587 Remote Similarity NPC252544
0.5867 Remote Similarity NPC221777
0.5867 Remote Similarity NPC48248
0.5867 Remote Similarity NPC473017
0.5862 Remote Similarity NPC272454
0.5862 Remote Similarity NPC178395
0.5862 Remote Similarity NPC26433
0.5862 Remote Similarity NPC292665
0.5862 Remote Similarity NPC301987
0.5862 Remote Similarity NPC159760
0.5862 Remote Similarity NPC149246
0.5862 Remote Similarity NPC35856
0.5862 Remote Similarity NPC115188
0.5862 Remote Similarity NPC179092
0.5862 Remote Similarity NPC244994
0.5862 Remote Similarity NPC222876
0.5857 Remote Similarity NPC307651
0.5855 Remote Similarity NPC473982
0.585 Remote Similarity NPC375356
0.585 Remote Similarity NPC85511
0.585 Remote Similarity NPC285394
0.5845 Remote Similarity NPC28951
0.5845 Remote Similarity NPC325646
0.5845 Remote Similarity NPC108288
0.5845 Remote Similarity NPC83718
0.5845 Remote Similarity NPC469843
0.584 Remote Similarity NPC194326
0.5839 Remote Similarity NPC265407

  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 NPC475082 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
0.7812 Intermediate Similarity NPD446 Clinical (unspecified phase)
0.7698 Intermediate Similarity NPD1246 Approved
0.7405 Intermediate Similarity NPD1245 Approved
0.7132 Intermediate Similarity NPD5277 Phase 2
0.695 Remote Similarity NPD6966 Discovery
0.6899 Remote Similarity NPD5278 Discontinued
0.6818 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6641 Remote Similarity NPD1237 Approved
0.6594 Remote Similarity NPD2345 Approved
0.6571 Remote Similarity NPD1877 Discontinued
0.6493 Remote Similarity NPD1279 Clinical (unspecified phase)
0.6467 Remote Similarity NPD7137 Phase 2
0.6463 Remote Similarity NPD5668 Clinical (unspecified phase)
0.6391 Remote Similarity NPD1317 Discontinued
0.6358 Remote Similarity NPD3494 Approved
0.6358 Remote Similarity NPD3492 Approved
0.6358 Remote Similarity NPD3493 Approved
0.6203 Remote Similarity NPD5049 Phase 3
0.6194 Remote Similarity NPD6831 Clinical (unspecified phase)
0.617 Remote Similarity NPD4196 Clinical (unspecified phase)
0.6142 Remote Similarity NPD9260 Approved
0.6127 Remote Similarity NPD7163 Clinical (unspecified phase)
0.6111 Remote Similarity NPD3356 Approved
0.6111 Remote Similarity NPD3355 Approved
0.6096 Remote Similarity NPD4099 Approved
0.6096 Remote Similarity NPD4100 Approved
0.609 Remote Similarity NPD745 Clinical (unspecified phase)
0.608 Remote Similarity NPD9256 Approved
0.608 Remote Similarity NPD9258 Approved
0.6061 Remote Similarity NPD1931 Clinical (unspecified phase)
0.6061 Remote Similarity NPD1930 Approved
0.6061 Remote Similarity NPD1929 Approved
0.6054 Remote Similarity NPD5740 Clinical (unspecified phase)
0.6054 Remote Similarity NPD2788 Approved
0.6054 Remote Similarity NPD6085 Phase 2
0.6043 Remote Similarity NPD690 Clinical (unspecified phase)
0.6043 Remote Similarity NPD5951 Approved
0.6039 Remote Similarity NPD2862 Discontinued
0.6037 Remote Similarity NPD1006 Clinical (unspecified phase)
0.6014 Remote Similarity NPD1104 Approved
0.6 Remote Similarity NPD5422 Clinical (unspecified phase)
0.5985 Remote Similarity NPD2181 Clinical (unspecified phase)
0.5969 Remote Similarity NPD5206 Clinical (unspecified phase)
0.5966 Remote Similarity NPD6734 Clinical (unspecified phase)
0.5954 Remote Similarity NPD2066 Phase 3
0.5915 Remote Similarity NPD2347 Approved
0.5912 Remote Similarity NPD7440 Discontinued
0.5899 Remote Similarity NPD6891 Phase 2
0.5882 Remote Similarity NPD2202 Clinical (unspecified phase)
0.5878 Remote Similarity NPD9495 Approved
0.5871 Remote Similarity NPD7305 Phase 1
0.5865 Remote Similarity NPD1932 Approved
0.585 Remote Similarity NPD5158 Clinical (unspecified phase)
0.585 Remote Similarity NPD5157 Phase 1
0.585 Remote Similarity NPD5159 Phase 2
0.5845 Remote Similarity NPD405 Clinical (unspecified phase)
0.5814 Remote Similarity NPD1202 Approved
0.5811 Remote Similarity NPD1888 Phase 1
0.5809 Remote Similarity NPD183 Approved
0.5804 Remote Similarity NPD7610 Discontinued
0.5796 Remote Similarity NPD2344 Approved
0.5793 Remote Similarity NPD5305 Approved
0.5793 Remote Similarity NPD5306 Approved
0.5789 Remote Similarity NPD3135 Clinical (unspecified phase)
0.5782 Remote Similarity NPD4878 Approved
0.5772 Remote Similarity NPD1470 Approved
0.5771 Remote Similarity NPD6597 Approved
0.5771 Remote Similarity NPD6598 Approved
0.5769 Remote Similarity NPD1693 Approved
0.5766 Remote Similarity NPD9267 Approved
0.5766 Remote Similarity NPD9263 Approved
0.5766 Remote Similarity NPD9264 Approved
0.576 Remote Similarity NPD9257 Approved
0.576 Remote Similarity NPD9259 Approved
0.5754 Remote Similarity NPD6990 Approved
0.5754 Remote Similarity NPD6989 Approved
0.5752 Remote Similarity NPD4404 Approved
0.5734 Remote Similarity NPD3797 Approved
0.5734 Remote Similarity NPD9493 Approved
0.5733 Remote Similarity NPD2798 Approved
0.5733 Remote Similarity NPD6007 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4980 Approved
0.5725 Remote Similarity NPD2329 Discontinued
0.5725 Remote Similarity NPD74 Approved
0.5725 Remote Similarity NPD9266 Approved
0.5725 Remote Similarity NPD2182 Approved
0.5724 Remote Similarity NPD4105 Approved
0.5724 Remote Similarity NPD5952 Clinical (unspecified phase)
0.5724 Remote Similarity NPD4102 Approved
0.5714 Remote Similarity NPD6659 Phase 2
0.5714 Remote Similarity NPD1609 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1201 Approved
0.5714 Remote Similarity NPD3449 Discontinued
0.5705 Remote Similarity NPD5886 Approved
0.5705 Remote Similarity NPD41 Approved
0.5704 Remote Similarity NPD2629 Approved
0.5692 Remote Similarity NPD5122 Clinical (unspecified phase)
0.5676 Remote Similarity NPD2722 Phase 1
0.5662 Remote Similarity NPD164 Approved
0.5658 Remote Similarity NPD7055 Discontinued
0.5657 Remote Similarity NPD6384 Phase 2
0.5657 Remote Similarity NPD6383 Clinical (unspecified phase)
0.5655 Remote Similarity NPD3798 Phase 3
0.5655 Remote Similarity NPD7330 Discontinued
0.5652 Remote Similarity NPD2309 Approved
0.565 Remote Similarity NPD5953 Discontinued
0.5646 Remote Similarity NPD4135 Approved
0.5646 Remote Similarity NPD4879 Approved
0.5646 Remote Similarity NPD4136 Approved
0.5646 Remote Similarity NPD4106 Approved
0.5643 Remote Similarity NPD4141 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7636 Approved
0.5625 Remote Similarity NPD800 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