Structure

Physi-Chem Properties

Molecular Weight:  278.22
Volume:  326.919
LogP:  3.738
LogD:  3.722
LogS:  -4.007
# Rotatable Bonds:  10
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.525
Synthetic Accessibility Score:  2.847
Fsp3:  0.667
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:  -4.611
MDCK Permeability:  2.356366894673556e-05
Pgp-inhibitor:  0.826
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.973
30% Bioavailability (F30%):  0.712

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.86
Plasma Protein Binding (PPB):  92.7265853881836%
Volume Distribution (VD):  0.828
Pgp-substrate:  3.1121368408203125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.216
CYP1A2-substrate:  0.249
CYP2C19-inhibitor:  0.416
CYP2C19-substrate:  0.311
CYP2C9-inhibitor:  0.726
CYP2C9-substrate:  0.979
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.319
CYP3A4-inhibitor:  0.194
CYP3A4-substrate:  0.189

ADMET: Excretion

Clearance (CL):  6.876
Half-life (T1/2):  0.868

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.312
Drug-inuced Liver Injury (DILI):  0.343
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.079
Skin Sensitization:  0.954
Carcinogencity:  0.106
Eye Corrosion:  0.964
Eye Irritation:  0.942
Respiratory Toxicity:  0.039

Download Data

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

  Natural Product: NPC262558

Natural Product ID:  NPC262558
Common Name*:   (5E,10Z)-6,10,14-Trimethylpentadeca-5,10-Diene-2,12-Dione
IUPAC Name:   (5E,10Z)-6,10,14-trimethylpentadeca-5,10-diene-2,12-dione
Synonyms:  
Standard InCHIKey:  WFIQWFJWGZPVFS-ZAYWLTRMSA-N
Standard InCHI:  InChI=1S/C18H30O2/c1-14(2)12-18(20)13-16(4)10-6-8-15(3)9-7-11-17(5)19/h9,13-14H,6-8,10-12H2,1-5H3/b15-9+,16-13-
SMILES:  CC(=O)CC/C=C(/CCC/C(=CC(=O)CC(C)C)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL446249
PubChem CID:   23426802
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO11479 Sargassum siliquastrum Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[15921416]
NPO11479 Sargassum siliquastrum Species Sargassaceae Eukaryota n.a. subtidal zone (0-2 m) off the southwestern shore of Jeju Island, Korea 2003-Apr PMID[18817444]
NPO11479 Sargassum siliquastrum Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[19006667]
NPO11479 Sargassum siliquastrum Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[21377877]
NPO11479 Sargassum siliquastrum Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[28720331]
NPO11479 Sargassum siliquastrum Species Sargassaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. EC50 = 3720.0 nM PMID[496698]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. EC50 = 14500.0 nM PMID[496698]

☑ 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 NPC262558 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 NPC8610
0.8542 High Similarity NPC32351
0.8478 Intermediate Similarity NPC166788
0.8478 Intermediate Similarity NPC191337
0.8444 Intermediate Similarity NPC301972
0.84 Intermediate Similarity NPC45283
0.8261 Intermediate Similarity NPC477686
0.82 Intermediate Similarity NPC471751
0.8163 Intermediate Similarity NPC228776
0.8163 Intermediate Similarity NPC176819
0.8163 Intermediate Similarity NPC118788
0.8163 Intermediate Similarity NPC163984
0.8163 Intermediate Similarity NPC58970
0.814 Intermediate Similarity NPC180840
0.8077 Intermediate Similarity NPC275472
0.8039 Intermediate Similarity NPC474141
0.8039 Intermediate Similarity NPC296311
0.8039 Intermediate Similarity NPC268564
0.7925 Intermediate Similarity NPC473733
0.7917 Intermediate Similarity NPC14917
0.7917 Intermediate Similarity NPC236355
0.7917 Intermediate Similarity NPC471752
0.7917 Intermediate Similarity NPC100380
0.7917 Intermediate Similarity NPC4079
0.7907 Intermediate Similarity NPC185839
0.7872 Intermediate Similarity NPC25771
0.7818 Intermediate Similarity NPC259261
0.78 Intermediate Similarity NPC15325
0.7778 Intermediate Similarity NPC193695
0.7755 Intermediate Similarity NPC91962
0.7692 Intermediate Similarity NPC23117
0.7674 Intermediate Similarity NPC38497
0.766 Intermediate Similarity NPC292463
0.766 Intermediate Similarity NPC216921
0.7647 Intermediate Similarity NPC27438
0.7647 Intermediate Similarity NPC64866
0.7636 Intermediate Similarity NPC311852
0.7636 Intermediate Similarity NPC94991
0.7636 Intermediate Similarity NPC266295
0.76 Intermediate Similarity NPC145311
0.7556 Intermediate Similarity NPC217923
0.7547 Intermediate Similarity NPC202850
0.7547 Intermediate Similarity NPC63396
0.7544 Intermediate Similarity NPC97322
0.75 Intermediate Similarity NPC471753
0.7451 Intermediate Similarity NPC20934
0.7451 Intermediate Similarity NPC225974
0.7451 Intermediate Similarity NPC288381
0.7407 Intermediate Similarity NPC188789
0.7391 Intermediate Similarity NPC111474
0.7368 Intermediate Similarity NPC25853
0.7358 Intermediate Similarity NPC14002
0.7358 Intermediate Similarity NPC37644
0.7333 Intermediate Similarity NPC155880
0.7333 Intermediate Similarity NPC92863
0.7321 Intermediate Similarity NPC30215
0.7308 Intermediate Similarity NPC477458
0.7292 Intermediate Similarity NPC106819
0.7288 Intermediate Similarity NPC473902
0.7273 Intermediate Similarity NPC20603
0.7241 Intermediate Similarity NPC475795
0.7222 Intermediate Similarity NPC5626
0.7222 Intermediate Similarity NPC189677
0.7209 Intermediate Similarity NPC12889
0.72 Intermediate Similarity NPC276009
0.72 Intermediate Similarity NPC195246
0.72 Intermediate Similarity NPC22098
0.7193 Intermediate Similarity NPC96551
0.7193 Intermediate Similarity NPC285594
0.7193 Intermediate Similarity NPC472304
0.7193 Intermediate Similarity NPC276764
0.7193 Intermediate Similarity NPC143834
0.7167 Intermediate Similarity NPC470688
0.7167 Intermediate Similarity NPC251118
0.7143 Intermediate Similarity NPC49575
0.7143 Intermediate Similarity NPC55004
0.7143 Intermediate Similarity NPC115385
0.7143 Intermediate Similarity NPC145755
0.7143 Intermediate Similarity NPC267626
0.7143 Intermediate Similarity NPC267514
0.7143 Intermediate Similarity NPC230823
0.7119 Intermediate Similarity NPC322457
0.7119 Intermediate Similarity NPC167256
0.7115 Intermediate Similarity NPC474391
0.7091 Intermediate Similarity NPC297280
0.7069 Intermediate Similarity NPC127582
0.7059 Intermediate Similarity NPC324812
0.7045 Intermediate Similarity NPC269641
0.7037 Intermediate Similarity NPC217188
0.7018 Intermediate Similarity NPC60772
0.7018 Intermediate Similarity NPC27610
0.7018 Intermediate Similarity NPC56905
0.7018 Intermediate Similarity NPC308108
0.7018 Intermediate Similarity NPC170799
0.7 Intermediate Similarity NPC212210
0.7 Intermediate Similarity NPC150162
0.7 Intermediate Similarity NPC474202
0.7 Intermediate Similarity NPC4638
0.7 Intermediate Similarity NPC474362
0.6981 Remote Similarity NPC48162
0.6981 Remote Similarity NPC234829
0.6977 Remote Similarity NPC266979
0.6949 Remote Similarity NPC260573
0.6949 Remote Similarity NPC60565
0.6949 Remote Similarity NPC213152
0.6949 Remote Similarity NPC64985
0.6923 Remote Similarity NPC267110
0.6909 Remote Similarity NPC100809
0.6909 Remote Similarity NPC209431
0.6897 Remote Similarity NPC278202
0.6889 Remote Similarity NPC92224
0.6852 Remote Similarity NPC151919
0.6852 Remote Similarity NPC170167
0.6852 Remote Similarity NPC216407
0.6842 Remote Similarity NPC283502
0.6842 Remote Similarity NPC192427
0.6842 Remote Similarity NPC281230
0.6842 Remote Similarity NPC192843
0.6833 Remote Similarity NPC155849
0.6833 Remote Similarity NPC190049
0.6833 Remote Similarity NPC165695
0.6833 Remote Similarity NPC288253
0.6833 Remote Similarity NPC32285
0.6825 Remote Similarity NPC469688
0.6825 Remote Similarity NPC87141
0.6825 Remote Similarity NPC155198
0.6825 Remote Similarity NPC260474
0.6825 Remote Similarity NPC188292
0.6825 Remote Similarity NPC469679
0.6786 Remote Similarity NPC477984
0.6774 Remote Similarity NPC137163
0.6731 Remote Similarity NPC471958
0.6727 Remote Similarity NPC69898
0.6727 Remote Similarity NPC295777
0.6724 Remote Similarity NPC281195
0.6721 Remote Similarity NPC475124
0.6721 Remote Similarity NPC169275
0.6721 Remote Similarity NPC52449
0.6721 Remote Similarity NPC6697
0.6721 Remote Similarity NPC285371
0.6719 Remote Similarity NPC139397
0.6719 Remote Similarity NPC477449
0.6719 Remote Similarity NPC256846
0.6719 Remote Similarity NPC477448
0.6719 Remote Similarity NPC469914
0.6667 Remote Similarity NPC148056
0.6667 Remote Similarity NPC244452
0.6667 Remote Similarity NPC475523
0.6667 Remote Similarity NPC12319
0.6667 Remote Similarity NPC113082
0.6667 Remote Similarity NPC325977
0.6667 Remote Similarity NPC228574
0.6667 Remote Similarity NPC64971
0.6667 Remote Similarity NPC101147
0.6667 Remote Similarity NPC294304
0.6667 Remote Similarity NPC18205
0.6615 Remote Similarity NPC203819
0.6615 Remote Similarity NPC265782
0.6615 Remote Similarity NPC318766
0.6615 Remote Similarity NPC251929
0.6615 Remote Similarity NPC307176
0.6615 Remote Similarity NPC260040
0.6615 Remote Similarity NPC2634
0.6613 Remote Similarity NPC470329
0.6613 Remote Similarity NPC474329
0.6613 Remote Similarity NPC474304
0.6607 Remote Similarity NPC474127
0.6607 Remote Similarity NPC317796
0.6607 Remote Similarity NPC322461
0.6596 Remote Similarity NPC266298
0.6562 Remote Similarity NPC470256
0.6562 Remote Similarity NPC310992
0.6562 Remote Similarity NPC476614
0.6557 Remote Similarity NPC477707
0.6557 Remote Similarity NPC477830
0.6557 Remote Similarity NPC197238
0.6557 Remote Similarity NPC202118
0.6552 Remote Similarity NPC299369
0.6552 Remote Similarity NPC165808
0.6552 Remote Similarity NPC200831
0.6552 Remote Similarity NPC268185
0.6552 Remote Similarity NPC224103
0.6538 Remote Similarity NPC308331
0.6538 Remote Similarity NPC128280
0.6531 Remote Similarity NPC7754
0.6531 Remote Similarity NPC270170
0.6531 Remote Similarity NPC33489
0.6531 Remote Similarity NPC188596
0.6515 Remote Similarity NPC474884
0.6515 Remote Similarity NPC181204
0.6515 Remote Similarity NPC474539
0.6515 Remote Similarity NPC133253
0.6515 Remote Similarity NPC190035
0.6515 Remote Similarity NPC54123
0.6508 Remote Similarity NPC308294
0.6508 Remote Similarity NPC197089
0.6508 Remote Similarity NPC142423
0.6481 Remote Similarity NPC27264
0.6481 Remote Similarity NPC289388
0.6481 Remote Similarity NPC329773

  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 NPC262558 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
0.7955 Intermediate Similarity NPD5783 Phase 3
0.7018 Intermediate Similarity NPD287 Approved
0.6774 Remote Similarity NPD7331 Phase 2
0.6719 Remote Similarity NPD4137 Phase 3
0.6615 Remote Similarity NPD4747 Approved
0.6615 Remote Similarity NPD4691 Approved
0.6552 Remote Similarity NPD8779 Phase 3
0.6515 Remote Similarity NPD5276 Approved
0.6491 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6383 Remote Similarity NPD319 Phase 1
0.6349 Remote Similarity NPD7341 Phase 2
0.6346 Remote Similarity NPD39 Approved
0.6346 Remote Similarity NPD3174 Discontinued
0.6324 Remote Similarity NPD4058 Approved
0.6324 Remote Similarity NPD5733 Approved
0.6324 Remote Similarity NPD4687 Approved
0.6316 Remote Similarity NPD539 Approved
0.6296 Remote Similarity NPD4220 Pre-registration
0.629 Remote Similarity NPD2664 Clinical (unspecified phase)
0.625 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6129 Remote Similarity NPD4191 Approved
0.6129 Remote Similarity NPD4194 Approved
0.6129 Remote Similarity NPD4192 Approved
0.6129 Remote Similarity NPD4193 Approved
0.6094 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6071 Remote Similarity NPD28 Approved
0.6071 Remote Similarity NPD29 Approved
0.6071 Remote Similarity NPD6927 Phase 3
0.6061 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6038 Remote Similarity NPD4222 Approved
0.6 Remote Similarity NPD3173 Approved
0.5962 Remote Similarity NPD5326 Phase 3
0.5909 Remote Similarity NPD3709 Clinical (unspecified phase)
0.5862 Remote Similarity NPD3172 Approved
0.5849 Remote Similarity NPD6096 Approved
0.5849 Remote Similarity NPD6097 Approved
0.5818 Remote Similarity NPD5343 Approved
0.5811 Remote Similarity NPD4695 Discontinued
0.5763 Remote Similarity NPD3194 Approved
0.5763 Remote Similarity NPD4266 Approved
0.5763 Remote Similarity NPD3196 Approved
0.5763 Remote Similarity NPD3195 Phase 2
0.5658 Remote Similarity NPD4221 Approved
0.5658 Remote Similarity NPD4223 Phase 3
0.5658 Remote Similarity NPD5209 Approved
0.56 Remote Similarity NPD8259 Clinical (unspecified phase)

  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