Structure

Physi-Chem Properties

Molecular Weight:  316.08
Volume:  323.974
LogP:  3.565
LogD:  2.161
LogS:  -4.106
# Rotatable Bonds:  6
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.633
Synthetic Accessibility Score:  3.947
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.165
MDCK Permeability:  1.4170442227623425e-05
Pgp-inhibitor:  0.13
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.584
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  100.51984405517578%
Volume Distribution (VD):  1.756
Pgp-substrate:  2.520124673843384%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.142
CYP2C19-inhibitor:  0.924
CYP2C19-substrate:  0.442
CYP2C9-inhibitor:  0.938
CYP2C9-substrate:  0.939
CYP2D6-inhibitor:  0.745
CYP2D6-substrate:  0.68
CYP3A4-inhibitor:  0.844
CYP3A4-substrate:  0.609

ADMET: Excretion

Clearance (CL):  1.454
Half-life (T1/2):  0.065

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.832
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.924
Rat Oral Acute Toxicity:  0.109
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.937
Carcinogencity:  0.519
Eye Corrosion:  0.894
Eye Irritation:  0.747
Respiratory Toxicity:  0.343

Download Data

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

  Natural Product: NPC475086

Natural Product ID:  NPC475086
Common Name*:   (+/-)-5-(1,2-Diacetoxyethyl)-2-(E)-Hept-5-Ene-1,3-Diynylthiophene
IUPAC Name:   [2-acetyloxy-2-[5-[(E)-hept-5-en-1,3-diynyl]thiophen-2-yl]ethyl] acetate
Synonyms:  
Standard InCHIKey:  SZRQIJOTIIDHCG-SNAWJCMRSA-N
Standard InCHI:  InChI=1S/C17H16O4S/c1-4-5-6-7-8-9-15-10-11-17(22-15)16(21-14(3)19)12-20-13(2)18/h4-5,10-11,16H,12H2,1-3H3/b5-4+
SMILES:  C/C=C/C#CC#Cc1ccc(s1)C(OC(=O)C)COC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL496641
PubChem CID:   44583856
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 = 0.66 ug.mL-1 PMID[540365]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 > 10.0 ug.mL-1 PMID[540365]

☑ 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 NPC475086 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
0.8545 High Similarity NPC32356
0.8077 Intermediate Similarity NPC474934
0.7573 Intermediate Similarity NPC2751
0.7477 Intermediate Similarity NPC472170
0.7387 Intermediate Similarity NPC472172
0.7297 Intermediate Similarity NPC472171
0.7297 Intermediate Similarity NPC475115
0.699 Remote Similarity NPC472169
0.6723 Remote Similarity NPC190955
0.6667 Remote Similarity NPC304760
0.6667 Remote Similarity NPC299367
0.6638 Remote Similarity NPC234305
0.6585 Remote Similarity NPC221877
0.6552 Remote Similarity NPC173019
0.6542 Remote Similarity NPC58616
0.6525 Remote Similarity NPC472919
0.6455 Remote Similarity NPC220893
0.6422 Remote Similarity NPC89377
0.6412 Remote Similarity NPC475082
0.6364 Remote Similarity NPC474364
0.6333 Remote Similarity NPC472315
0.6333 Remote Similarity NPC474376
0.6333 Remote Similarity NPC472316
0.6333 Remote Similarity NPC475203
0.6306 Remote Similarity NPC173443
0.6303 Remote Similarity NPC85977
0.63 Remote Similarity NPC105991
0.6293 Remote Similarity NPC475954
0.6281 Remote Similarity NPC277788
0.626 Remote Similarity NPC476003
0.625 Remote Similarity NPC185501
0.6239 Remote Similarity NPC472318
0.6239 Remote Similarity NPC98911
0.622 Remote Similarity NPC476014
0.622 Remote Similarity NPC476031
0.6218 Remote Similarity NPC474365
0.6218 Remote Similarity NPC301943
0.6207 Remote Similarity NPC325499
0.6198 Remote Similarity NPC136962
0.6195 Remote Similarity NPC119631
0.6116 Remote Similarity NPC269457
0.6111 Remote Similarity NPC307651
0.6098 Remote Similarity NPC469636
0.6083 Remote Similarity NPC91820
0.6083 Remote Similarity NPC82426
0.608 Remote Similarity NPC185840
0.6063 Remote Similarity NPC210092
0.6033 Remote Similarity NPC242913
0.6033 Remote Similarity NPC148060
0.6033 Remote Similarity NPC280616
0.6033 Remote Similarity NPC171831
0.6032 Remote Similarity NPC265002
0.6032 Remote Similarity NPC474176
0.6017 Remote Similarity NPC78701
0.6017 Remote Similarity NPC35448
0.6016 Remote Similarity NPC216387
0.6 Remote Similarity NPC60373
0.6 Remote Similarity NPC291619
0.6 Remote Similarity NPC154905
0.6 Remote Similarity NPC470794
0.6 Remote Similarity NPC101503
0.6 Remote Similarity NPC254958
0.5984 Remote Similarity NPC474363
0.5981 Remote Similarity NPC8981
0.5968 Remote Similarity NPC83628
0.5968 Remote Similarity NPC265407
0.5966 Remote Similarity NPC146351
0.5966 Remote Similarity NPC325497
0.5965 Remote Similarity NPC213156
0.5965 Remote Similarity NPC240108
0.5952 Remote Similarity NPC234376
0.5952 Remote Similarity NPC474314
0.5948 Remote Similarity NPC23453
0.5935 Remote Similarity NPC37115
0.5932 Remote Similarity NPC249912
0.5932 Remote Similarity NPC276775
0.5932 Remote Similarity NPC92754
0.592 Remote Similarity NPC174099
0.5909 Remote Similarity NPC307163
0.5891 Remote Similarity NPC473507
0.5882 Remote Similarity NPC225060
0.5873 Remote Similarity NPC264784
0.5865 Remote Similarity NPC229600
0.5854 Remote Similarity NPC473855
0.5854 Remote Similarity NPC17537
0.584 Remote Similarity NPC17417
0.584 Remote Similarity NPC10251
0.584 Remote Similarity NPC469511
0.5833 Remote Similarity NPC132725
0.5833 Remote Similarity NPC170484
0.582 Remote Similarity NPC160382
0.5818 Remote Similarity NPC103387
0.5818 Remote Similarity NPC106313
0.5818 Remote Similarity NPC323103
0.5814 Remote Similarity NPC474685
0.5814 Remote Similarity NPC469509
0.5809 Remote Similarity NPC470008
0.5809 Remote Similarity NPC246166
0.5806 Remote Similarity NPC326447
0.5804 Remote Similarity NPC475710
0.5802 Remote Similarity NPC469574
0.5794 Remote Similarity NPC196246
0.5794 Remote Similarity NPC251854
0.5794 Remote Similarity NPC214067
0.5794 Remote Similarity NPC93084
0.5789 Remote Similarity NPC476183
0.5785 Remote Similarity NPC70624
0.5781 Remote Similarity NPC128368
0.5781 Remote Similarity NPC161611
0.578 Remote Similarity NPC121800
0.5772 Remote Similarity NPC283546
0.5769 Remote Similarity NPC149691
0.5766 Remote Similarity NPC270507
0.5766 Remote Similarity NPC471895
0.5763 Remote Similarity NPC5472
0.5763 Remote Similarity NPC130398
0.576 Remote Similarity NPC56493
0.576 Remote Similarity NPC151530
0.576 Remote Similarity NPC157473
0.5748 Remote Similarity NPC231251
0.5748 Remote Similarity NPC474157
0.5748 Remote Similarity NPC25067
0.5748 Remote Similarity NPC1082
0.5748 Remote Similarity NPC30563
0.5748 Remote Similarity NPC88868
0.5748 Remote Similarity NPC305912
0.5746 Remote Similarity NPC476184
0.5746 Remote Similarity NPC476281
0.5736 Remote Similarity NPC308744
0.5736 Remote Similarity NPC172525
0.5727 Remote Similarity NPC89950
0.5727 Remote Similarity NPC165212
0.5726 Remote Similarity NPC152384
0.5726 Remote Similarity NPC37714
0.5726 Remote Similarity NPC238115
0.5725 Remote Similarity NPC190298
0.5725 Remote Similarity NPC474987
0.5714 Remote Similarity NPC269023
0.5714 Remote Similarity NPC99846
0.5714 Remote Similarity NPC291837
0.5714 Remote Similarity NPC281604
0.5714 Remote Similarity NPC175376
0.5704 Remote Similarity NPC114845
0.5703 Remote Similarity NPC82899
0.5703 Remote Similarity NPC158282
0.5703 Remote Similarity NPC270699
0.5702 Remote Similarity NPC96625
0.5702 Remote Similarity NPC169050
0.5702 Remote Similarity NPC118343
0.5702 Remote Similarity NPC286608
0.5702 Remote Similarity NPC203925
0.5702 Remote Similarity NPC171843
0.5701 Remote Similarity NPC175393
0.5691 Remote Similarity NPC179686
0.5691 Remote Similarity NPC89886
0.569 Remote Similarity NPC166487
0.568 Remote Similarity NPC119271
0.568 Remote Similarity NPC30594
0.568 Remote Similarity NPC176971
0.568 Remote Similarity NPC37622
0.568 Remote Similarity NPC477251
0.5678 Remote Similarity NPC300455
0.5674 Remote Similarity NPC23908
0.5669 Remote Similarity NPC474148
0.5669 Remote Similarity NPC276061
0.5669 Remote Similarity NPC273837
0.5667 Remote Similarity NPC270654
0.5662 Remote Similarity NPC476278
0.5656 Remote Similarity NPC42211
0.5656 Remote Similarity NPC469481
0.5652 Remote Similarity NPC476033
0.5652 Remote Similarity NPC85830
0.5649 Remote Similarity NPC11821
0.5649 Remote Similarity NPC100353
0.5645 Remote Similarity NPC109637
0.5645 Remote Similarity NPC269644
0.5639 Remote Similarity NPC159916
0.5639 Remote Similarity NPC309434
0.5639 Remote Similarity NPC293424
0.5639 Remote Similarity NPC277460
0.563 Remote Similarity NPC50872
0.563 Remote Similarity NPC267064
0.5625 Remote Similarity NPC308619
0.5625 Remote Similarity NPC183700
0.5625 Remote Similarity NPC43584
0.5625 Remote Similarity NPC127491
0.5625 Remote Similarity NPC63345
0.5625 Remote Similarity NPC324835
0.562 Remote Similarity NPC476260
0.562 Remote Similarity NPC138798
0.562 Remote Similarity NPC471466
0.562 Remote Similarity NPC279379
0.562 Remote Similarity NPC476241
0.5615 Remote Similarity NPC153053
0.5612 Remote Similarity NPC61181
0.561 Remote Similarity NPC188895
0.5606 Remote Similarity NPC76844
0.5606 Remote Similarity NPC123559
0.5606 Remote Similarity NPC281277
0.5603 Remote Similarity NPC475508

  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 NPC475086 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
0.704 Intermediate Similarity NPD1877 Discontinued
0.6855 Remote Similarity NPD446 Clinical (unspecified phase)
0.6692 Remote Similarity NPD4404 Approved
0.6618 Remote Similarity NPD41 Approved
0.6618 Remote Similarity NPD5886 Approved
0.6522 Remote Similarity NPD2862 Discontinued
0.6423 Remote Similarity NPD1279 Clinical (unspecified phase)
0.6403 Remote Similarity NPD7137 Phase 2
0.6311 Remote Similarity NPD5278 Discontinued
0.6299 Remote Similarity NPD2347 Approved
0.6232 Remote Similarity NPD2202 Clinical (unspecified phase)
0.619 Remote Similarity NPD1246 Approved
0.6129 Remote Similarity NPD2181 Clinical (unspecified phase)
0.6122 Remote Similarity NPD6890 Discontinued
0.6111 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6087 Remote Similarity NPD4248 Discontinued
0.608 Remote Similarity NPD969 Suspended
0.6074 Remote Similarity NPD5740 Clinical (unspecified phase)
0.6074 Remote Similarity NPD6085 Phase 2
0.6061 Remote Similarity NPD4480 Approved
0.6048 Remote Similarity NPD2067 Discontinued
0.6032 Remote Similarity NPD5277 Phase 2
0.6016 Remote Similarity NPD1358 Approved
0.5974 Remote Similarity NPD3492 Approved
0.5974 Remote Similarity NPD3494 Approved
0.5974 Remote Similarity NPD3493 Approved
0.5954 Remote Similarity NPD1245 Approved
0.5948 Remote Similarity NPD1006 Clinical (unspecified phase)
0.5891 Remote Similarity NPD4198 Discontinued
0.5874 Remote Similarity NPD7305 Phase 1
0.5874 Remote Similarity NPD5580 Discontinued
0.584 Remote Similarity NPD2182 Approved
0.5811 Remote Similarity NPD1979 Approved
0.5806 Remote Similarity NPD3134 Approved
0.5789 Remote Similarity NPD6813 Clinical (unspecified phase)
0.5782 Remote Similarity NPD1978 Approved
0.5782 Remote Similarity NPD7835 Discontinued
0.5775 Remote Similarity NPD4340 Discontinued
0.5735 Remote Similarity NPD7876 Discontinued
0.5725 Remote Similarity NPD694 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3535 Clinical (unspecified phase)
0.5702 Remote Similarity NPD1282 Approved
0.5702 Remote Similarity NPD1238 Approved
0.5683 Remote Similarity NPD4006 Discontinued
0.5683 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5676 Remote Similarity NPD7976 Clinical (unspecified phase)
0.5671 Remote Similarity NPD6597 Approved
0.5671 Remote Similarity NPD6598 Approved
0.5662 Remote Similarity NPD4232 Approved
0.5658 Remote Similarity NPD2900 Approved
0.5658 Remote Similarity NPD2901 Approved
0.5655 Remote Similarity NPD2164 Clinical (unspecified phase)
0.5608 Remote Similarity NPD1652 Phase 2
0.5603 Remote Similarity NPD6966 Discovery
0.56 Remote Similarity NPD7440 Discontinued

  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