Natural Product: NPC216921

Natural Product ID:  NPC216921
Common Name:   Zerumbone
IUPAC Name:   (2E,6E,10E)-2,6,9,9-tetramethylcycloundeca-2,6,10-trien-1-one
Synonyms:   Zerumbone
Molecular Formula:   C15H22O
Standard InCHIKey:  GIHNTRQPEMKFKO-SKTNYSRSSA-N
Standard InCHI:  InChI=1S/C15H22O/c1-12-6-5-7-13(2)14(16)9-11-15(3,4)10-8-12/h7-9,11H,5-6,10H2,1-4H3/b11-9+,12-8+,13-7+
Canonical SMILES:  C/C/1=CCC(C)(C)/C=C/C(=O)/C(=C/CC1)/C
First Find Year:  
Max Developmental Stage:  
Synthetic Gene Cluster:   ;

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO20995 Syringa pinnafolia Species Oleaceae Eukaryota HerDing*
NPO27791 Zingiber zerumbet Species Zingiberaceae Eukaryota HerDing*
NPO27791 Zingiber zerumbet Species Zingiberaceae Eukaryota Rhizomes PMID[15997145]
NPO31107 Zingiber cassumunar Species Zingiberaceae Eukaryota Rhizomes PMID[1804548]
NPO1183 Ligularia macrophylla Species Asteraceae Eukaryota UNPD*
NPO9510 Penicillium leucopus Species Aspergillaceae Eukaryota UNPD*
NPO3069 Quercus agrifolia Species Fagaceae Eukaryota UNPD*
NPO29538 Curcumae radix NA NA NA TCMSP*
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota TM-MC*
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota TM-MC*
NPO4682 Lindera aggregata Species Lauraceae Eukaryota TM-MC*
NPO13346 Lindera strichnifolia Species Tineidae Eukaryota TM-MC*
NPO27791 Zingiber zerumbet Species Zingiberaceae Eukaryota TCMID*
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota TCMID*
NPO20995 Syringa pinnafolia Species Oleaceae Eukaryota TCMID*
NPO9035 Verbascum thapsus Species Scrophulariaceae Eukaryota UNPD*
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota PMID[15270556]
NPO27625 Buddleja globosa Species Scrophulariaceae Eukaryota Roots London PMID[10514305]
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota HerDing*
NPO12458 Zingiber aromaticum Species Zingiberaceae Eukaryota Rhizomes DOI[10.1080/10575639708043725]

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT5237 Individual Protein Sensor histidine kinase yycG Bacillus subtilis (strain 168) IC50 > 500 ug/ml 17157007
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100 ug/ml 17157007
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 100 ug/ml 17157007
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens IC50 = 21800 nM 15270556
NPT110 Individual Protein Cytochrome P450 2D6 Homo sapiens IC50 > 100000 nM 15270556
NPT1896 Individual Protein Zinc finger protein GLI1 Homo sapiens IC50 = 7100 nM 19309080
NPT5108 Individual Protein Zinc finger protein GLI2 Homo sapiens IC50 = 910 nM 19309080
NPT2 Others Unspecified Ratio IC50 = 7 19309080
NPT2 Others Unspecified Inhibition = 0 % 10514305
NPT183 Individual Protein Arachidonate 5-lipoxygenase Rattus norvegicus Inhibition = 0 % 10514305
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Inhibition = -4.84 % 23062825
NPT67 Individual Protein Cholinesterase Equus caballus Inhibition = 4.2 % 23062825
NPT83 Cell Line MCF7 Homo sapiens IC50 = 9.67 ug/ml 26459207
NPT65 Cell Line HepG2 Homo sapiens IC50 = 13.34 ug/ml 26459207
NPT2 Others Unspecified IC50 = 6.05 ug/ml 26459207
NPT4468 Cell Line P338 Mus musculus IC50 = 2.63 ug/ml 26459207
NPT660 Cell Line SW480 Homo sapiens IC50 = 3.15 ug/ml 26459207
NPT165 Cell Line HeLa Homo sapiens IC50 = 3.15 ug/ml 26459207
NPT81 Cell Line A549 Homo sapiens Inhibition = 48 % 26681550
NPT81 Cell Line A549 Homo sapiens Inhibition = 69 % 26681550

  Similar Natural Products 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 NPC216921 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
0.8696 High Similarity NPC118788
0.8163 Intermediate Similarity NPC37644
0.8095 Intermediate Similarity NPC217923
0.8049 Intermediate Similarity NPC185839
0.8 Intermediate Similarity NPC269641
0.8 Intermediate Similarity NPC477686
0.7917 Intermediate Similarity NPC228776
0.7907 Intermediate Similarity NPC111474
0.7857 Intermediate Similarity NPC180840
0.7826 Intermediate Similarity NPC191337
0.7826 Intermediate Similarity NPC166788
0.7805 Intermediate Similarity NPC38497
0.78 Intermediate Similarity NPC14002
0.78 Intermediate Similarity NPC296311
0.78 Intermediate Similarity NPC23117
0.7778 Intermediate Similarity NPC301972
0.775 Intermediate Similarity NPC12889
0.766 Intermediate Similarity NPC262558
0.766 Intermediate Similarity NPC100380
0.766 Intermediate Similarity NPC8610
0.7647 Intermediate Similarity NPC5626
0.7609 Intermediate Similarity NPC471753
0.7551 Intermediate Similarity NPC15325
0.7547 Intermediate Similarity NPC71755
0.75 Intermediate Similarity NPC18205
0.75 Intermediate Similarity NPC266979
0.75 Intermediate Similarity NPC12319
0.7451 Intermediate Similarity NPC295777
0.7451 Intermediate Similarity NPC69898
0.7442 Intermediate Similarity NPC155880
0.7442 Intermediate Similarity NPC92863
0.7407 Intermediate Similarity NPC311852
0.74 Intermediate Similarity NPC64866
0.7347 Intermediate Similarity NPC145311
0.7292 Intermediate Similarity NPC471752
0.725 Intermediate Similarity NPC66577
0.7234 Intermediate Similarity NPC145755
0.7234 Intermediate Similarity NPC25771
0.7234 Intermediate Similarity NPC267514
0.7209 Intermediate Similarity NPC24833
0.72 Intermediate Similarity NPC58970
0.72 Intermediate Similarity NPC32351
0.72 Intermediate Similarity NPC176819
0.72 Intermediate Similarity NPC163984
0.7111 Intermediate Similarity NPC113082
0.7111 Intermediate Similarity NPC101147
0.7091 Intermediate Similarity NPC60772
0.7059 Intermediate Similarity NPC30433
0.7021 Intermediate Similarity NPC292463
0.7018 Intermediate Similarity NPC228574
0.7018 Intermediate Similarity NPC294304
0.6981 Remote Similarity NPC474127
0.6964 Remote Similarity NPC96551
0.6964 Remote Similarity NPC285594
0.6964 Remote Similarity NPC203233
0.6957 Remote Similarity NPC7754
0.6957 Remote Similarity NPC33489
0.6957 Remote Similarity NPC270170
0.6923 Remote Similarity NPC471751
0.6909 Remote Similarity NPC115385
0.6897 Remote Similarity NPC288253
0.6889 Remote Similarity NPC33761
0.6863 Remote Similarity NPC225974
0.6842 Remote Similarity NPC25853
0.6818 Remote Similarity NPC254764
0.6818 Remote Similarity NPC279300
0.6809 Remote Similarity NPC208936
0.6809 Remote Similarity NPC67920
0.6809 Remote Similarity NPC287397
0.6809 Remote Similarity NPC298710
0.68 Remote Similarity NPC324812
0.6792 Remote Similarity NPC268564
0.6792 Remote Similarity NPC45283
0.6786 Remote Similarity NPC30215
0.6786 Remote Similarity NPC94991
0.6786 Remote Similarity NPC266295
0.675 Remote Similarity NPC155900
0.6739 Remote Similarity NPC323278
0.6735 Remote Similarity NPC474202
0.6735 Remote Similarity NPC474362
0.6724 Remote Similarity NPC97322
0.6724 Remote Similarity NPC260573
0.6667 Remote Similarity NPC259261
0.6667 Remote Similarity NPC106819
0.6667 Remote Similarity NPC130923
0.6667 Remote Similarity NPC38455
0.6667 Remote Similarity NPC251118
0.661 Remote Similarity NPC165695
0.661 Remote Similarity NPC167256
0.661 Remote Similarity NPC32285
0.6607 Remote Similarity NPC22019
0.6607 Remote Similarity NPC281986
0.6607 Remote Similarity NPC208749
0.6607 Remote Similarity NPC321568
0.6604 Remote Similarity NPC46565
0.6604 Remote Similarity NPC229046
0.66 Remote Similarity NPC4079
0.66 Remote Similarity NPC236355
0.66 Remote Similarity NPC14917
0.6591 Remote Similarity NPC75204
0.6552 Remote Similarity NPC127582
0.6545 Remote Similarity NPC275472
0.6545 Remote Similarity NPC297280
0.6538 Remote Similarity NPC474391
0.6538 Remote Similarity NPC20934
0.6538 Remote Similarity NPC288381
0.6538 Remote Similarity NPC27264
0.6538 Remote Similarity NPC236338
0.6538 Remote Similarity NPC220191
0.6531 Remote Similarity NPC6963
0.6531 Remote Similarity NPC304079
0.65 Remote Similarity NPC4638
0.65 Remote Similarity NPC212210
0.6491 Remote Similarity NPC308108
0.6491 Remote Similarity NPC27610
0.6491 Remote Similarity NPC281195
0.6491 Remote Similarity NPC170799
0.6491 Remote Similarity NPC56905
0.6481 Remote Similarity NPC474805
0.6481 Remote Similarity NPC474141
0.6471 Remote Similarity NPC91962
0.6471 Remote Similarity NPC471958
0.6458 Remote Similarity NPC51758
0.6458 Remote Similarity NPC68889
0.6458 Remote Similarity NPC209279
0.6458 Remote Similarity NPC108494
0.6458 Remote Similarity NPC180871
0.6458 Remote Similarity NPC67761
0.6458 Remote Similarity NPC88079
0.6458 Remote Similarity NPC194586
0.6452 Remote Similarity NPC106613
0.6444 Remote Similarity NPC220061
0.6441 Remote Similarity NPC475795
0.6441 Remote Similarity NPC213152
0.6429 Remote Similarity NPC473733
0.6429 Remote Similarity NPC206088
0.6415 Remote Similarity NPC27438
0.6415 Remote Similarity NPC477458
0.6415 Remote Similarity NPC234829
0.6415 Remote Similarity NPC148056
0.6415 Remote Similarity NPC22329
0.64 Remote Similarity NPC270706
0.6383 Remote Similarity NPC56917
0.6364 Remote Similarity NPC300121
0.6364 Remote Similarity NPC189677
0.6364 Remote Similarity NPC322461
0.6364 Remote Similarity NPC72258
0.6364 Remote Similarity NPC317796
0.6349 Remote Similarity NPC260474
0.6349 Remote Similarity NPC87141
0.6349 Remote Similarity NPC188292
0.6346 Remote Similarity NPC267110
0.6346 Remote Similarity NPC15912
0.6341 Remote Similarity NPC138113
0.6333 Remote Similarity NPC322457
0.6316 Remote Similarity NPC267626
0.6316 Remote Similarity NPC193695
0.6316 Remote Similarity NPC268185
0.6316 Remote Similarity NPC281230
0.6316 Remote Similarity NPC230823
0.6316 Remote Similarity NPC283502
0.6316 Remote Similarity NPC192843
0.6316 Remote Similarity NPC55004
0.6316 Remote Similarity NPC49575
0.6296 Remote Similarity NPC151919
0.6296 Remote Similarity NPC137396
0.629 Remote Similarity NPC176171
0.629 Remote Similarity NPC92327
0.6279 Remote Similarity NPC304788
0.6275 Remote Similarity NPC276009
0.6275 Remote Similarity NPC308331
0.6275 Remote Similarity NPC128280
0.6275 Remote Similarity NPC195246
0.6275 Remote Similarity NPC22098
0.625 Remote Similarity NPC188596
0.625 Remote Similarity NPC136473
0.625 Remote Similarity NPC188789
0.625 Remote Similarity NPC473603
0.625 Remote Similarity NPC256846
0.625 Remote Similarity NPC476059
0.623 Remote Similarity NPC6697
0.623 Remote Similarity NPC475124
0.623 Remote Similarity NPC285371
0.623 Remote Similarity NPC473902
0.6226 Remote Similarity NPC116906
0.6226 Remote Similarity NPC15789
0.6226 Remote Similarity NPC221467
0.619 Remote Similarity NPC475523
0.619 Remote Similarity NPC60288
0.619 Remote Similarity NPC176107
0.6167 Remote Similarity NPC64985
0.614 Remote Similarity NPC325977
0.614 Remote Similarity NPC20603
0.6129 Remote Similarity NPC470329
0.6129 Remote Similarity NPC470688
0.6111 Remote Similarity NPC43053
0.6102 Remote Similarity NPC472304
0.6102 Remote Similarity NPC276764
0.6102 Remote Similarity NPC143834
0.6094 Remote Similarity NPC117804

  Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC216921 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
0.7674 Intermediate Similarity NPD5783 Phase 3
0.6491 Remote Similarity NPD287 Approved
0.6364 Remote Similarity NPD539 Approved
0.6346 Remote Similarity NPD4220 Pre-registration
0.6034 Remote Similarity NPD8779 Phase 3
0.5909 Remote Similarity NPD4691 Approved
0.5902 Remote Similarity NPD4193 Approved
0.5902 Remote Similarity NPD4191 Approved
0.5902 Remote Similarity NPD4192 Approved
0.5902 Remote Similarity NPD4194 Approved
0.5882 Remote Similarity NPD4058 Approved
0.5781 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5769 Remote Similarity NPD4222 Approved
0.5769 Remote Similarity NPD3174 Discontinued
0.5769 Remote Similarity NPD39 Approved
0.5758 Remote Similarity NPD4137 Phase 3
0.5692 Remote Similarity NPD3709 Clinical (unspecified phase)
0.5686 Remote Similarity NPD5326 Phase 3
0.5672 Remote Similarity NPD4747 Approved
0.5652 Remote Similarity NPD4687 Approved

Structure

External Identifiers

PubChem CID   5470187
ChEMBL   CHEMBL245412
ZINC  

Physicochemical Properties

Molecular Weight:  218.17
ALogP:  3.4791
MLogP:  3
XLogP:  4.143
# Rotatable Bonds:  4
Polar Surface Area:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  16

Download Data

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