Structure

Physi-Chem Properties

Molecular Weight:  216.12
Volume:  249.825
LogP:  3.188
LogD:  2.673
LogS:  -3.671
# Rotatable Bonds:  4
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.579
Synthetic Accessibility Score:  3.473
Fsp3:  0.357
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:  -4.463
MDCK Permeability:  3.178463884978555e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  100.92003631591797%
Volume Distribution (VD):  0.261
Pgp-substrate:  1.036953330039978%

ADMET: Metabolism

CYP1A2-inhibitor:  0.34
CYP1A2-substrate:  0.161
CYP2C19-inhibitor:  0.841
CYP2C19-substrate:  0.197
CYP2C9-inhibitor:  0.86
CYP2C9-substrate:  0.999
CYP2D6-inhibitor:  0.828
CYP2D6-substrate:  0.909
CYP3A4-inhibitor:  0.681
CYP3A4-substrate:  0.096

ADMET: Excretion

Clearance (CL):  1.333
Half-life (T1/2):  0.835

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.977
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.62
Rat Oral Acute Toxicity:  0.189
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.925
Carcinogencity:  0.784
Eye Corrosion:  0.982
Eye Irritation:  0.981
Respiratory Toxicity:  0.945

Download Data

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

  Natural Product: NPC42304

Natural Product ID:  NPC42304
Common Name*:   (7E,11E)-Tetradecadiene-5,9-Diynoic Acid
IUPAC Name:   (7E,11E)-tetradeca-7,11-dien-5,9-diynoic acid
Synonyms:  
Standard InCHIKey:  IHXAUHSVYVDJQO-DYWGDJMRSA-N
Standard InCHI:  InChI=1S/C14H16O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14(15)16/h3-4,7-8H,2,11-13H2,1H3,(H,15,16)/b4-3+,8-7+
SMILES:  CC/C=C/C#C/C=C/C#CCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL498234
PubChem CID:   10822604
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO33149 oceanapia sp. Species Phloeodictyidae Eukaryota n.a. n.a. n.a. PMID[10843591]
NPO33149 oceanapia sp. Species Phloeodictyidae Eukaryota n.a. n.a. n.a. PMID[15921437]
NPO33149 oceanapia sp. Species Phloeodictyidae Eukaryota n.a. n.a. n.a. PMID[7769396]
NPO33149 oceanapia sp. Species Phloeodictyidae Eukaryota n.a. micronesian n.a. PMID[9514015]

☑ 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
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 6.5 mm PMID[516330]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 7.0 mm PMID[516330]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 9.0 mm PMID[516330]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 7.5 mm PMID[516330]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 10.0 mm PMID[516330]
NPT20 Organism Candida albicans Candida albicans IZ = 8.5 mm PMID[516330]
NPT19 Organism Escherichia coli Escherichia coli IZ = 8.5 mm PMID[516330]
NPT19 Organism Escherichia coli Escherichia coli IZ = 12.0 mm PMID[516330]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 8.5 mm PMID[516330]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 13.0 mm PMID[516330]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 11.0 mm PMID[516330]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 9.5 mm PMID[516330]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 13.5 mm PMID[516330]

☑ 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 NPC42304 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
0.9149 High Similarity NPC28205
0.9149 High Similarity NPC284212
0.8889 High Similarity NPC117572
0.8571 High Similarity NPC129458
0.8571 High Similarity NPC303765
0.8511 High Similarity NPC91495
0.8431 Intermediate Similarity NPC274290
0.8431 Intermediate Similarity NPC473863
0.84 Intermediate Similarity NPC10081
0.84 Intermediate Similarity NPC225066
0.8333 Intermediate Similarity NPC5413
0.8333 Intermediate Similarity NPC149821
0.8269 Intermediate Similarity NPC187777
0.8269 Intermediate Similarity NPC179764
0.8163 Intermediate Similarity NPC59051
0.8125 Intermediate Similarity NPC207292
0.8077 Intermediate Similarity NPC45626
0.8077 Intermediate Similarity NPC54766
0.8043 Intermediate Similarity NPC270796
0.8 Intermediate Similarity NPC48162
0.7963 Intermediate Similarity NPC329819
0.7843 Intermediate Similarity NPC281245
0.7843 Intermediate Similarity NPC92114
0.7778 Intermediate Similarity NPC225929
0.7692 Intermediate Similarity NPC1813
0.7692 Intermediate Similarity NPC294548
0.7692 Intermediate Similarity NPC70387
0.7692 Intermediate Similarity NPC139029
0.7692 Intermediate Similarity NPC36061
0.7692 Intermediate Similarity NPC321062
0.7636 Intermediate Similarity NPC267817
0.7547 Intermediate Similarity NPC322461
0.7547 Intermediate Similarity NPC88966
0.7547 Intermediate Similarity NPC281972
0.7547 Intermediate Similarity NPC25417
0.7547 Intermediate Similarity NPC154245
0.7547 Intermediate Similarity NPC32467
0.7547 Intermediate Similarity NPC290563
0.7547 Intermediate Similarity NPC85813
0.7547 Intermediate Similarity NPC87564
0.7547 Intermediate Similarity NPC261831
0.7547 Intermediate Similarity NPC424
0.7547 Intermediate Similarity NPC6095
0.75 Intermediate Similarity NPC18357
0.7407 Intermediate Similarity NPC477984
0.7407 Intermediate Similarity NPC474672
0.7368 Intermediate Similarity NPC235242
0.7308 Intermediate Similarity NPC470411
0.7308 Intermediate Similarity NPC470410
0.7308 Intermediate Similarity NPC470412
0.7308 Intermediate Similarity NPC178586
0.7288 Intermediate Similarity NPC226592
0.7273 Intermediate Similarity NPC327388
0.7273 Intermediate Similarity NPC477201
0.7273 Intermediate Similarity NPC325977
0.7273 Intermediate Similarity NPC18951
0.7255 Intermediate Similarity NPC163345
0.7222 Intermediate Similarity NPC137538
0.7143 Intermediate Similarity NPC323597
0.7143 Intermediate Similarity NPC323436
0.7143 Intermediate Similarity NPC323498
0.7143 Intermediate Similarity NPC211752
0.7115 Intermediate Similarity NPC224227
0.7111 Intermediate Similarity NPC158179
0.7091 Intermediate Similarity NPC67367
0.7091 Intermediate Similarity NPC52264
0.7059 Intermediate Similarity NPC180534
0.7037 Intermediate Similarity NPC284224
0.7 Intermediate Similarity NPC470320
0.6981 Remote Similarity NPC477777
0.6981 Remote Similarity NPC262968
0.6957 Remote Similarity NPC73245
0.6909 Remote Similarity NPC300121
0.6897 Remote Similarity NPC274927
0.6897 Remote Similarity NPC329249
0.6897 Remote Similarity NPC322002
0.6897 Remote Similarity NPC329550
0.6897 Remote Similarity NPC106851
0.6852 Remote Similarity NPC161366
0.6852 Remote Similarity NPC477779
0.6842 Remote Similarity NPC472445
0.678 Remote Similarity NPC243532
0.678 Remote Similarity NPC174447
0.678 Remote Similarity NPC81896
0.678 Remote Similarity NPC251042
0.678 Remote Similarity NPC327112
0.678 Remote Similarity NPC328311
0.678 Remote Similarity NPC122521
0.678 Remote Similarity NPC321919
0.6727 Remote Similarity NPC39633
0.6727 Remote Similarity NPC139545
0.6727 Remote Similarity NPC309606
0.6724 Remote Similarity NPC469373
0.6724 Remote Similarity NPC34416
0.6667 Remote Similarity NPC474362
0.6667 Remote Similarity NPC328776
0.6667 Remote Similarity NPC474202
0.6667 Remote Similarity NPC113293
0.6667 Remote Similarity NPC320305
0.6667 Remote Similarity NPC321838
0.6667 Remote Similarity NPC201939
0.6667 Remote Similarity NPC40082
0.6667 Remote Similarity NPC123357
0.6667 Remote Similarity NPC477829
0.661 Remote Similarity NPC318306
0.6607 Remote Similarity NPC474127
0.6596 Remote Similarity NPC40434
0.6596 Remote Similarity NPC34873
0.6596 Remote Similarity NPC155880
0.6596 Remote Similarity NPC92863
0.6557 Remote Similarity NPC29697
0.6557 Remote Similarity NPC322457
0.6545 Remote Similarity NPC216407
0.6538 Remote Similarity NPC87137
0.6531 Remote Similarity NPC163746
0.6531 Remote Similarity NPC103286
0.6515 Remote Similarity NPC477981
0.6515 Remote Similarity NPC477983
0.6491 Remote Similarity NPC223677
0.6491 Remote Similarity NPC10316
0.6491 Remote Similarity NPC228473
0.6491 Remote Similarity NPC28779
0.6491 Remote Similarity NPC200845
0.6491 Remote Similarity NPC128061
0.6481 Remote Similarity NPC473487
0.6471 Remote Similarity NPC108195
0.6471 Remote Similarity NPC304079
0.6471 Remote Similarity NPC6963
0.6452 Remote Similarity NPC328089
0.6452 Remote Similarity NPC68343
0.6429 Remote Similarity NPC71761
0.6415 Remote Similarity NPC216130
0.64 Remote Similarity NPC187922
0.64 Remote Similarity NPC71317
0.64 Remote Similarity NPC129972
0.64 Remote Similarity NPC301528
0.6393 Remote Similarity NPC325929
0.6393 Remote Similarity NPC174560
0.6393 Remote Similarity NPC475984
0.6393 Remote Similarity NPC66460
0.6393 Remote Similarity NPC125312
0.6393 Remote Similarity NPC271282
0.6379 Remote Similarity NPC472808
0.6379 Remote Similarity NPC324224
0.6364 Remote Similarity NPC43053
0.6364 Remote Similarity NPC15129
0.6349 Remote Similarity NPC478098
0.6349 Remote Similarity NPC320642
0.6349 Remote Similarity NPC245947
0.6349 Remote Similarity NPC318420
0.6349 Remote Similarity NPC476657
0.6349 Remote Similarity NPC255863
0.6349 Remote Similarity NPC326268
0.6349 Remote Similarity NPC476654
0.6349 Remote Similarity NPC476655
0.6349 Remote Similarity NPC478099
0.6349 Remote Similarity NPC136164
0.6349 Remote Similarity NPC317881
0.6349 Remote Similarity NPC323045
0.6346 Remote Similarity NPC276825
0.6333 Remote Similarity NPC222852
0.6333 Remote Similarity NPC322186
0.6327 Remote Similarity NPC8270
0.6316 Remote Similarity NPC87394
0.6296 Remote Similarity NPC135698
0.6296 Remote Similarity NPC207815
0.6296 Remote Similarity NPC302310
0.629 Remote Similarity NPC68110
0.629 Remote Similarity NPC470965
0.6279 Remote Similarity NPC174368
0.6275 Remote Similarity NPC19305
0.6275 Remote Similarity NPC255837
0.6271 Remote Similarity NPC265551
0.6271 Remote Similarity NPC44542
0.6271 Remote Similarity NPC212730
0.625 Remote Similarity NPC476656
0.625 Remote Similarity NPC151919
0.625 Remote Similarity NPC477982
0.625 Remote Similarity NPC478101
0.625 Remote Similarity NPC476659
0.625 Remote Similarity NPC170167
0.625 Remote Similarity NPC473705
0.625 Remote Similarity NPC226511
0.6226 Remote Similarity NPC477776
0.6226 Remote Similarity NPC308331
0.6207 Remote Similarity NPC152668
0.6207 Remote Similarity NPC474513
0.6207 Remote Similarity NPC470963
0.6207 Remote Similarity NPC146551
0.6207 Remote Similarity NPC474913
0.62 Remote Similarity NPC221250
0.619 Remote Similarity NPC234767
0.6182 Remote Similarity NPC27264
0.6182 Remote Similarity NPC328784
0.6182 Remote Similarity NPC221467
0.6182 Remote Similarity NPC225974
0.6182 Remote Similarity NPC474391
0.6182 Remote Similarity NPC291437
0.6167 Remote Similarity NPC478096
0.6167 Remote Similarity NPC471619

  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 NPC42304 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
0.8889 High Similarity NPD4222 Approved
0.8333 Intermediate Similarity NPD3173 Approved
0.8085 Intermediate Similarity NPD39 Approved
0.8043 Intermediate Similarity NPD5326 Phase 3
0.7708 Intermediate Similarity NPD3174 Discontinued
0.7692 Intermediate Similarity NPD3172 Approved
0.7547 Intermediate Similarity NPD3194 Approved
0.7547 Intermediate Similarity NPD3196 Approved
0.7547 Intermediate Similarity NPD3195 Phase 2
0.7547 Intermediate Similarity NPD4266 Approved
0.74 Intermediate Similarity NPD5343 Approved
0.7059 Intermediate Similarity NPD622 Approved
0.6981 Remote Similarity NPD29 Approved
0.6981 Remote Similarity NPD28 Approved
0.68 Remote Similarity NPD6097 Approved
0.68 Remote Similarity NPD6096 Approved
0.678 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6724 Remote Similarity NPD6109 Phase 1
0.6452 Remote Similarity NPD3197 Phase 1
0.6327 Remote Similarity NPD9635 Discontinued
0.6296 Remote Similarity NPD4220 Pre-registration
0.6275 Remote Similarity NPD9411 Phase 1
0.6154 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6071 Remote Similarity NPD6927 Phase 3
0.58 Remote Similarity NPD633 Phase 3
0.58 Remote Similarity NPD9448 Phase 2
0.58 Remote Similarity NPD5783 Phase 3
0.58 Remote Similarity NPD9450 Approved
0.58 Remote Similarity NPD77 Approved
0.5763 Remote Similarity NPD8971 Approved
0.5745 Remote Similarity NPD8857 Approved
0.5741 Remote Similarity NPD4265 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