Structure

Physi-Chem Properties

Molecular Weight:  365.18
Volume:  370.623
LogP:  0.994
LogD:  0.923
LogS:  -2.051
# Rotatable Bonds:  0
TPSA:  93.14
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.506
Synthetic Accessibility Score:  5.471
Fsp3:  0.632
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.666
MDCK Permeability:  2.58258733083494e-05
Pgp-inhibitor:  0.958
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.961
30% Bioavailability (F30%):  0.742

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.536
Plasma Protein Binding (PPB):  31.77488899230957%
Volume Distribution (VD):  1.983
Pgp-substrate:  69.53636169433594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.073
CYP1A2-substrate:  0.161
CYP2C19-inhibitor:  0.16
CYP2C19-substrate:  0.842
CYP2C9-inhibitor:  0.053
CYP2C9-substrate:  0.208
CYP2D6-inhibitor:  0.548
CYP2D6-substrate:  0.742
CYP3A4-inhibitor:  0.129
CYP3A4-substrate:  0.543

ADMET: Excretion

Clearance (CL):  4.954
Half-life (T1/2):  0.701

ADMET: Toxicity

hERG Blockers:  0.055
Human Hepatotoxicity (H-HT):  0.247
Drug-inuced Liver Injury (DILI):  0.468
AMES Toxicity:  0.975
Rat Oral Acute Toxicity:  0.738
Maximum Recommended Daily Dose:  0.887
Skin Sensitization:  0.947
Carcinogencity:  0.323
Eye Corrosion:  0.005
Eye Irritation:  0.016
Respiratory Toxicity:  0.055

Download Data

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

  Natural Product: NPC196073

Natural Product ID:  NPC196073
Common Name*:   Senkirkine
IUPAC Name:   (1R,4E,6R,7R,11Z)-4-ethylidene-7-hydroxy-6,7,14-trimethyl-2,9-dioxa-14-azabicyclo[9.5.1]heptadec-11-ene-3,8,17-trione
Synonyms:   Senkirkine
Standard InCHIKey:  HPDHKHMHQGCNPE-HKZJLVJOSA-N
Standard InCHI:  InChI=1S/C19H27NO6/c1-5-13-10-12(2)19(3,24)18(23)25-11-14-6-8-20(4)9-7-15(16(14)21)26-17(13)22/h5-6,12,15,24H,7-11H2,1-4H3/b13-5+,14-6-/t12-,15-,19-/m1/s1
SMILES:  C/C=C/1C[C@@H](C)[C@@](C)(O)C(=O)OCC2=CCN(CC[C@@H](OC1=O)C2=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469650
PubChem CID:   6442498
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[10543912]
NPO33066 senecio anonymus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3210016]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[32881525]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO523 Tussilago farfara 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
NPT2319 Cell Line A204 Homo sapiens IC50 = 260.0 ug.mL-1 PMID[537926]
NPT364 Organism Lactuca sativa Lactuca sativa Inhibition < 50.0 % PMID[537927]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 116.0 % PMID[537927]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 105.0 % PMID[537927]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi Activity = 53.0 % PMID[537927]
NPT348 Organism Myzus persicae Myzus persicae Activity = 35.0 % PMID[537927]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 > 50.0 microg/cm2 PMID[537927]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis EC50 > 50.0 microg/cm2 PMID[537927]

☑ 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 NPC196073 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
1.0 High Similarity NPC195435
0.9806 High Similarity NPC474497
0.9806 High Similarity NPC275100
0.9352 High Similarity NPC156336
0.9352 High Similarity NPC200412
0.9352 High Similarity NPC120599
0.8333 Intermediate Similarity NPC106791
0.8333 Intermediate Similarity NPC201889
0.8304 Intermediate Similarity NPC193471
0.8304 Intermediate Similarity NPC130124
0.8017 Intermediate Similarity NPC284656
0.7965 Intermediate Similarity NPC47857
0.7965 Intermediate Similarity NPC181510
0.7965 Intermediate Similarity NPC168758
0.7815 Intermediate Similarity NPC23963
0.7712 Intermediate Similarity NPC235625
0.7652 Intermediate Similarity NPC30911
0.7652 Intermediate Similarity NPC316984
0.7434 Intermediate Similarity NPC64168
0.7345 Intermediate Similarity NPC173690
0.7345 Intermediate Similarity NPC279833
0.7345 Intermediate Similarity NPC6271
0.7345 Intermediate Similarity NPC80439
0.7193 Intermediate Similarity NPC475945
0.7193 Intermediate Similarity NPC475871
0.7168 Intermediate Similarity NPC474742
0.7143 Intermediate Similarity NPC471144
0.713 Intermediate Similarity NPC474741
0.7105 Intermediate Similarity NPC149371
0.7105 Intermediate Similarity NPC474747
0.7043 Intermediate Similarity NPC472755
0.7018 Intermediate Similarity NPC164598
0.7018 Intermediate Similarity NPC47880
0.7018 Intermediate Similarity NPC474339
0.7018 Intermediate Similarity NPC472753
0.6967 Remote Similarity NPC30196
0.696 Remote Similarity NPC156379
0.696 Remote Similarity NPC475383
0.6957 Remote Similarity NPC472754
0.6935 Remote Similarity NPC241050
0.693 Remote Similarity NPC475949
0.6911 Remote Similarity NPC475642
0.6911 Remote Similarity NPC6531
0.6903 Remote Similarity NPC476344
0.6897 Remote Similarity NPC475873
0.6891 Remote Similarity NPC38154
0.6875 Remote Similarity NPC150041
0.687 Remote Similarity NPC476270
0.687 Remote Similarity NPC46998
0.687 Remote Similarity NPC201718
0.687 Remote Similarity NPC185141
0.687 Remote Similarity NPC110443
0.687 Remote Similarity NPC133907
0.687 Remote Similarity NPC128733
0.6864 Remote Similarity NPC477513
0.686 Remote Similarity NPC1111
0.686 Remote Similarity NPC60432
0.686 Remote Similarity NPC261750
0.685 Remote Similarity NPC318445
0.685 Remote Similarity NPC316133
0.6818 Remote Similarity NPC51004
0.6814 Remote Similarity NPC17585
0.6803 Remote Similarity NPC469597
0.6757 Remote Similarity NPC20713
0.6757 Remote Similarity NPC30515
0.6752 Remote Similarity NPC68001
0.6752 Remote Similarity NPC199831
0.6752 Remote Similarity NPC474828
0.6752 Remote Similarity NPC474827
0.6742 Remote Similarity NPC316401
0.6727 Remote Similarity NPC307411
0.6726 Remote Similarity NPC475900
0.6726 Remote Similarity NPC471142
0.6724 Remote Similarity NPC15993
0.6696 Remote Similarity NPC179746
0.6696 Remote Similarity NPC476300
0.6696 Remote Similarity NPC475912
0.6696 Remote Similarity NPC81419
0.6696 Remote Similarity NPC161855
0.6695 Remote Similarity NPC472756
0.6695 Remote Similarity NPC100487
0.6695 Remote Similarity NPC203659
0.6667 Remote Similarity NPC476009
0.6667 Remote Similarity NPC471148
0.6667 Remote Similarity NPC473291
0.6667 Remote Similarity NPC320019
0.6667 Remote Similarity NPC324017
0.6667 Remote Similarity NPC473619
0.6667 Remote Similarity NPC476004
0.6667 Remote Similarity NPC316228
0.6667 Remote Similarity NPC477921
0.6667 Remote Similarity NPC474761
0.6642 Remote Similarity NPC120420
0.664 Remote Similarity NPC471146
0.664 Remote Similarity NPC471145
0.6639 Remote Similarity NPC475608
0.6639 Remote Similarity NPC474431
0.6639 Remote Similarity NPC474411
0.6639 Remote Similarity NPC21713
0.6638 Remote Similarity NPC288876
0.6638 Remote Similarity NPC477512
0.6637 Remote Similarity NPC474035
0.6637 Remote Similarity NPC81386
0.6637 Remote Similarity NPC121825
0.6636 Remote Similarity NPC153805
0.6636 Remote Similarity NPC475902
0.6636 Remote Similarity NPC202672
0.661 Remote Similarity NPC472747
0.661 Remote Similarity NPC472750
0.661 Remote Similarity NPC110989
0.6609 Remote Similarity NPC40812
0.6607 Remote Similarity NPC184463
0.6607 Remote Similarity NPC208886
0.6607 Remote Similarity NPC12172
0.6607 Remote Similarity NPC473321
0.6593 Remote Similarity NPC99864
0.6587 Remote Similarity NPC475401
0.6583 Remote Similarity NPC266514
0.6583 Remote Similarity NPC26617
0.6581 Remote Similarity NPC477511
0.6581 Remote Similarity NPC264477
0.6579 Remote Similarity NPC14961
0.6579 Remote Similarity NPC270013
0.6579 Remote Similarity NPC477922
0.6579 Remote Similarity NPC475659
0.6579 Remote Similarity NPC36954
0.6555 Remote Similarity NPC472748
0.6552 Remote Similarity NPC83895
0.6552 Remote Similarity NPC187761
0.6549 Remote Similarity NPC288240
0.6549 Remote Similarity NPC162205
0.6549 Remote Similarity NPC469645
0.6549 Remote Similarity NPC469692
0.6549 Remote Similarity NPC212486
0.6549 Remote Similarity NPC273579
0.6549 Remote Similarity NPC295204
0.6545 Remote Similarity NPC248602
0.6545 Remote Similarity NPC473248
0.6535 Remote Similarity NPC477092
0.6529 Remote Similarity NPC474099
0.6525 Remote Similarity NPC225353
0.6522 Remote Similarity NPC158416
0.6522 Remote Similarity NPC473859
0.6522 Remote Similarity NPC76862
0.6522 Remote Similarity NPC39859
0.6522 Remote Similarity NPC470883
0.6522 Remote Similarity NPC476275
0.6514 Remote Similarity NPC137033
0.6514 Remote Similarity NPC21469
0.6508 Remote Similarity NPC475305
0.6504 Remote Similarity NPC317107
0.65 Remote Similarity NPC472751
0.65 Remote Similarity NPC271269
0.65 Remote Similarity NPC472749
0.6496 Remote Similarity NPC469551
0.6491 Remote Similarity NPC190294
0.6491 Remote Similarity NPC469632
0.6486 Remote Similarity NPC281516
0.6486 Remote Similarity NPC153570
0.6486 Remote Similarity NPC474471
0.6486 Remote Similarity NPC227379
0.6484 Remote Similarity NPC477143
0.6484 Remote Similarity NPC477140
0.6481 Remote Similarity NPC11620
0.6466 Remote Similarity NPC245521
0.6466 Remote Similarity NPC52820
0.6462 Remote Similarity NPC314629
0.6462 Remote Similarity NPC280498
0.646 Remote Similarity NPC329952
0.646 Remote Similarity NPC219874
0.6455 Remote Similarity NPC164393
0.6455 Remote Similarity NPC261721
0.6452 Remote Similarity NPC66108
0.6452 Remote Similarity NPC317687
0.6446 Remote Similarity NPC254538
0.6446 Remote Similarity NPC474716
0.6446 Remote Similarity NPC474285
0.6439 Remote Similarity NPC314282
0.6435 Remote Similarity NPC474947
0.6435 Remote Similarity NPC272050
0.6429 Remote Similarity NPC474951
0.6429 Remote Similarity NPC87306
0.6429 Remote Similarity NPC173926
0.6423 Remote Similarity NPC477103
0.6423 Remote Similarity NPC5103
0.6422 Remote Similarity NPC474251
0.6417 Remote Similarity NPC477510
0.6417 Remote Similarity NPC471143
0.641 Remote Similarity NPC300584
0.641 Remote Similarity NPC473326
0.641 Remote Similarity NPC308567
0.641 Remote Similarity NPC255592
0.641 Remote Similarity NPC261377
0.6404 Remote Similarity NPC165383
0.6404 Remote Similarity NPC135776
0.6396 Remote Similarity NPC471738
0.6396 Remote Similarity NPC231889
0.6393 Remote Similarity NPC70235
0.6393 Remote Similarity NPC264819
0.6387 Remote Similarity NPC195510

  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 NPC196073 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
0.7652 Intermediate Similarity NPD2204 Approved
0.685 Remote Similarity NPD7642 Approved
0.6667 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6641 Remote Similarity NPD8080 Discontinued
0.6617 Remote Similarity NPD7260 Phase 2
0.6593 Remote Similarity NPD8415 Approved
0.6583 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6562 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6489 Remote Similarity NPD8273 Phase 1
0.6489 Remote Similarity NPD8451 Approved
0.6457 Remote Similarity NPD7641 Discontinued
0.6444 Remote Similarity NPD6845 Suspended
0.6439 Remote Similarity NPD8448 Approved
0.6308 Remote Similarity NPD6921 Approved
0.6296 Remote Similarity NPD8390 Approved
0.6296 Remote Similarity NPD8391 Approved
0.6296 Remote Similarity NPD8392 Approved
0.629 Remote Similarity NPD6371 Approved
0.6288 Remote Similarity NPD8299 Approved
0.6288 Remote Similarity NPD8341 Approved
0.6288 Remote Similarity NPD8342 Approved
0.6288 Remote Similarity NPD8340 Approved
0.625 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6228 Remote Similarity NPD46 Approved
0.6228 Remote Similarity NPD6698 Approved
0.6212 Remote Similarity NPD7829 Approved
0.6212 Remote Similarity NPD7830 Approved
0.6197 Remote Similarity NPD8384 Approved
0.6182 Remote Similarity NPD6110 Phase 1
0.6174 Remote Similarity NPD7983 Approved
0.6087 Remote Similarity NPD7838 Discovery
0.6061 Remote Similarity NPD8444 Approved
0.6017 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5878 Remote Similarity NPD7500 Approved
0.5865 Remote Similarity NPD6319 Approved
0.5865 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5833 Remote Similarity NPD4228 Discovery
0.5821 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5821 Remote Similarity NPD6908 Approved
0.5821 Remote Similarity NPD6909 Approved
0.5798 Remote Similarity NPD5282 Discontinued
0.5789 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5781 Remote Similarity NPD6421 Discontinued
0.5778 Remote Similarity NPD7623 Phase 3
0.5778 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5772 Remote Similarity NPD5344 Discontinued
0.5748 Remote Similarity NPD6686 Approved
0.5741 Remote Similarity NPD1452 Discontinued
0.5738 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5738 Remote Similarity NPD4225 Approved
0.5736 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5735 Remote Similarity NPD7604 Phase 2
0.5724 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5778 Approved
0.5714 Remote Similarity NPD5779 Approved
0.5683 Remote Similarity NPD8337 Approved
0.5683 Remote Similarity NPD8336 Approved
0.5678 Remote Similarity NPD5785 Approved
0.5677 Remote Similarity NPD8414 Discontinued
0.5667 Remote Similarity NPD2575 Approved
0.5664 Remote Similarity NPD5209 Approved
0.5649 Remote Similarity NPD4632 Approved
0.5649 Remote Similarity NPD1376 Discontinued
0.5625 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5615 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5612 Remote Similarity NPD8074 Phase 3
0.5612 Remote Similarity NPD7746 Phase 1
0.5612 Remote Similarity NPD7747 Phase 1
0.56 Remote Similarity NPD8086 Approved
0.56 Remote Similarity NPD8083 Approved
0.56 Remote Similarity NPD8139 Approved
0.56 Remote Similarity NPD8138 Approved
0.56 Remote Similarity NPD8084 Approved
0.56 Remote Similarity NPD8085 Approved
0.56 Remote Similarity NPD8082 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