Structure

Physi-Chem Properties

Molecular Weight:  346.06
Volume:  333.02
LogP:  4.376
LogD:  2.209
LogS:  -4.693
# Rotatable Bonds:  7
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.551
Synthetic Accessibility Score:  3.637
Fsp3:  0.389
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.527
MDCK Permeability:  4.05191931349691e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.351
20% Bioavailability (F20%):  0.034
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.62813568115234%
Volume Distribution (VD):  0.437
Pgp-substrate:  0.9586905837059021%

ADMET: Metabolism

CYP1A2-inhibitor:  0.496
CYP1A2-substrate:  0.191
CYP2C19-inhibitor:  0.906
CYP2C19-substrate:  0.454
CYP2C9-inhibitor:  0.902
CYP2C9-substrate:  0.999
CYP2D6-inhibitor:  0.874
CYP2D6-substrate:  0.916
CYP3A4-inhibitor:  0.822
CYP3A4-substrate:  0.076

ADMET: Excretion

Clearance (CL):  1.023
Half-life (T1/2):  0.68

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.978
Drug-inuced Liver Injury (DILI):  0.988
AMES Toxicity:  0.671
Rat Oral Acute Toxicity:  0.099
Maximum Recommended Daily Dose:  0.06
Skin Sensitization:  0.962
Carcinogencity:  0.58
Eye Corrosion:  0.963
Eye Irritation:  0.962
Respiratory Toxicity:  0.843

Download Data

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

  Natural Product: NPC225066

Natural Product ID:  NPC225066
Common Name*:   (9E,17E)-18-Bromooctadeca-9,17-Dien-5,7,15-Triynoic Acid
IUPAC Name:   (9E,17E)-18-bromooctadeca-9,17-dien-5,7,15-triynoic acid
Synonyms:  
Standard InCHIKey:  FBQBLKRYQBDOAU-UUUWWEMDSA-N
Standard InCHI:  InChI=1S/C18H19BrO2/c19-17-15-13-11-9-7-5-3-1-2-4-6-8-10-12-14-16-18(20)21/h1-2,15,17H,3,5,7,9,12,14,16H2,(H,20,21)/b2-1+,17-15+
SMILES:  Br/C=C/C#CCCCC/C=C/C#CC#CCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL476874
PubChem CID:   21762914
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
NPO24623 Xestospongia muta Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[1431940]
NPO24623 Xestospongia muta Species Petrosiidae 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
NPT202 Individual Protein Protease Human immunodeficiency virus 1 IC50 = 8000.0 nM PMID[547107]

☑ 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 NPC225066 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 NPC10081
0.9796 High Similarity NPC129458
0.9796 High Similarity NPC303765
0.9608 High Similarity NPC45626
0.9074 High Similarity NPC267817
0.8519 High Similarity NPC474672
0.8462 Intermediate Similarity NPC28205
0.8462 Intermediate Similarity NPC284212
0.84 Intermediate Similarity NPC42304
0.8235 Intermediate Similarity NPC91495
0.8235 Intermediate Similarity NPC207292
0.82 Intermediate Similarity NPC117572
0.8182 Intermediate Similarity NPC274290
0.8182 Intermediate Similarity NPC473863
0.8182 Intermediate Similarity NPC54766
0.8077 Intermediate Similarity NPC149821
0.8077 Intermediate Similarity NPC5413
0.8036 Intermediate Similarity NPC187777
0.8036 Intermediate Similarity NPC179764
0.7925 Intermediate Similarity NPC59051
0.7778 Intermediate Similarity NPC48162
0.7759 Intermediate Similarity NPC329819
0.7636 Intermediate Similarity NPC18357
0.7636 Intermediate Similarity NPC92114
0.7586 Intermediate Similarity NPC225929
0.75 Intermediate Similarity NPC139029
0.75 Intermediate Similarity NPC294548
0.75 Intermediate Similarity NPC321062
0.75 Intermediate Similarity NPC36061
0.75 Intermediate Similarity NPC1813
0.75 Intermediate Similarity NPC70387
0.7451 Intermediate Similarity NPC270796
0.7368 Intermediate Similarity NPC290563
0.7368 Intermediate Similarity NPC281972
0.7368 Intermediate Similarity NPC25417
0.7368 Intermediate Similarity NPC32467
0.7368 Intermediate Similarity NPC6095
0.7368 Intermediate Similarity NPC87564
0.7368 Intermediate Similarity NPC85813
0.7368 Intermediate Similarity NPC322461
0.7368 Intermediate Similarity NPC88966
0.7368 Intermediate Similarity NPC261831
0.7368 Intermediate Similarity NPC424
0.7368 Intermediate Similarity NPC154245
0.7321 Intermediate Similarity NPC281245
0.7241 Intermediate Similarity NPC477984
0.7213 Intermediate Similarity NPC235242
0.7143 Intermediate Similarity NPC470412
0.7143 Intermediate Similarity NPC470410
0.7119 Intermediate Similarity NPC477201
0.7119 Intermediate Similarity NPC325977
0.7119 Intermediate Similarity NPC327388
0.7119 Intermediate Similarity NPC18951
0.7 Intermediate Similarity NPC323498
0.7 Intermediate Similarity NPC211752
0.7 Intermediate Similarity NPC323436
0.7 Intermediate Similarity NPC323597
0.6964 Remote Similarity NPC473768
0.6964 Remote Similarity NPC224227
0.6909 Remote Similarity NPC180534
0.6897 Remote Similarity NPC284224
0.6875 Remote Similarity NPC470320
0.6875 Remote Similarity NPC226592
0.6842 Remote Similarity NPC178586
0.6842 Remote Similarity NPC470411
0.6842 Remote Similarity NPC262968
0.6825 Remote Similarity NPC477829
0.678 Remote Similarity NPC137538
0.6774 Remote Similarity NPC274927
0.6774 Remote Similarity NPC329550
0.6774 Remote Similarity NPC106851
0.6774 Remote Similarity NPC329249
0.6724 Remote Similarity NPC161366
0.6667 Remote Similarity NPC243532
0.6667 Remote Similarity NPC251042
0.6667 Remote Similarity NPC81896
0.6667 Remote Similarity NPC52264
0.6667 Remote Similarity NPC327112
0.6667 Remote Similarity NPC321919
0.6667 Remote Similarity NPC122521
0.6667 Remote Similarity NPC328311
0.6667 Remote Similarity NPC174447
0.6613 Remote Similarity NPC34416
0.6613 Remote Similarity NPC469373
0.661 Remote Similarity NPC71761
0.661 Remote Similarity NPC309606
0.661 Remote Similarity NPC139545
0.661 Remote Similarity NPC39633
0.66 Remote Similarity NPC158179
0.6562 Remote Similarity NPC320305
0.6562 Remote Similarity NPC125312
0.6562 Remote Similarity NPC201939
0.6562 Remote Similarity NPC328776
0.6562 Remote Similarity NPC174560
0.6562 Remote Similarity NPC475984
0.6562 Remote Similarity NPC321838
0.6562 Remote Similarity NPC40082
0.6508 Remote Similarity NPC322002
0.65 Remote Similarity NPC300121
0.6491 Remote Similarity NPC163345
0.6471 Remote Similarity NPC53302
0.6462 Remote Similarity NPC470965
0.6462 Remote Similarity NPC322457
0.6462 Remote Similarity NPC29697
0.6452 Remote Similarity NPC472445
0.6441 Remote Similarity NPC477779
0.6429 Remote Similarity NPC477981
0.6429 Remote Similarity NPC477983
0.6393 Remote Similarity NPC128061
0.6393 Remote Similarity NPC67367
0.6393 Remote Similarity NPC152668
0.6393 Remote Similarity NPC474513
0.6393 Remote Similarity NPC223677
0.6393 Remote Similarity NPC28779
0.6393 Remote Similarity NPC10316
0.6393 Remote Similarity NPC228473
0.6393 Remote Similarity NPC146551
0.6393 Remote Similarity NPC200845
0.6393 Remote Similarity NPC470963
0.6364 Remote Similarity NPC328089
0.6364 Remote Similarity NPC108195
0.6364 Remote Similarity NPC68343
0.6308 Remote Similarity NPC271282
0.6308 Remote Similarity NPC325929
0.6308 Remote Similarity NPC66460
0.6308 Remote Similarity NPC113293
0.629 Remote Similarity NPC311648
0.629 Remote Similarity NPC470964
0.6271 Remote Similarity NPC129263
0.6271 Remote Similarity NPC477777
0.6269 Remote Similarity NPC320642
0.6269 Remote Similarity NPC245947
0.6269 Remote Similarity NPC476657
0.6269 Remote Similarity NPC255863
0.6269 Remote Similarity NPC323477
0.6269 Remote Similarity NPC476654
0.6269 Remote Similarity NPC318420
0.6269 Remote Similarity NPC326268
0.6269 Remote Similarity NPC323045
0.6269 Remote Similarity NPC317881
0.6269 Remote Similarity NPC136164
0.6269 Remote Similarity NPC476655
0.625 Remote Similarity NPC474202
0.625 Remote Similarity NPC222852
0.625 Remote Similarity NPC276825
0.625 Remote Similarity NPC318306
0.625 Remote Similarity NPC474362
0.623 Remote Similarity NPC87394
0.6226 Remote Similarity NPC27444
0.6226 Remote Similarity NPC103236
0.6226 Remote Similarity NPC329762
0.6207 Remote Similarity NPC475153
0.6207 Remote Similarity NPC207815
0.6207 Remote Similarity NPC302310
0.619 Remote Similarity NPC265551
0.619 Remote Similarity NPC212730
0.619 Remote Similarity NPC594
0.619 Remote Similarity NPC44542
0.619 Remote Similarity NPC48968
0.6176 Remote Similarity NPC476659
0.6176 Remote Similarity NPC477982
0.6176 Remote Similarity NPC328653
0.6176 Remote Similarity NPC476656
0.6167 Remote Similarity NPC216407
0.6167 Remote Similarity NPC473705
0.6154 Remote Similarity NPC73245
0.6154 Remote Similarity NPC155880
0.6154 Remote Similarity NPC92863
0.614 Remote Similarity NPC157096
0.6111 Remote Similarity NPC163746
0.6111 Remote Similarity NPC103286
0.6102 Remote Similarity NPC474391
0.6102 Remote Similarity NPC473487
0.6094 Remote Similarity NPC325734
0.6087 Remote Similarity NPC49863
0.6087 Remote Similarity NPC330426
0.6087 Remote Similarity NPC478100
0.6087 Remote Similarity NPC148192
0.6087 Remote Similarity NPC22101
0.6087 Remote Similarity NPC478097
0.6087 Remote Similarity NPC104537
0.6087 Remote Similarity NPC26500
0.6087 Remote Similarity NPC99619
0.6087 Remote Similarity NPC271921
0.6087 Remote Similarity NPC127091
0.6081 Remote Similarity NPC470899
0.6066 Remote Similarity NPC477724
0.6066 Remote Similarity NPC187361
0.6066 Remote Similarity NPC26102
0.6066 Remote Similarity NPC217188
0.6066 Remote Similarity NPC61177
0.6066 Remote Similarity NPC34577
0.6034 Remote Similarity NPC216130
0.6032 Remote Similarity NPC472808
0.6032 Remote Similarity NPC324224
0.6029 Remote Similarity NPC478098
0.6029 Remote Similarity NPC478099
0.6 Remote Similarity NPC141481
0.6 Remote Similarity NPC477980
0.6 Remote Similarity NPC149668

  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 NPC225066 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
0.82 Intermediate Similarity NPD4222 Approved
0.8077 Intermediate Similarity NPD3173 Approved
0.7843 Intermediate Similarity NPD39 Approved
0.75 Intermediate Similarity NPD3174 Discontinued
0.75 Intermediate Similarity NPD3172 Approved
0.7451 Intermediate Similarity NPD5326 Phase 3
0.7368 Intermediate Similarity NPD3195 Phase 2
0.7368 Intermediate Similarity NPD3194 Approved
0.7368 Intermediate Similarity NPD3196 Approved
0.7368 Intermediate Similarity NPD4266 Approved
0.6909 Remote Similarity NPD622 Approved
0.6909 Remote Similarity NPD5343 Approved
0.6842 Remote Similarity NPD29 Approved
0.6842 Remote Similarity NPD28 Approved
0.6667 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6364 Remote Similarity NPD6096 Approved
0.6364 Remote Similarity NPD3197 Phase 1
0.6364 Remote Similarity NPD6097 Approved
0.6349 Remote Similarity NPD6109 Phase 1
0.6087 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5932 Remote Similarity NPD4220 Pre-registration
0.5738 Remote Similarity NPD6927 Phase 3
0.5636 Remote Similarity NPD9635 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