Structure

Physi-Chem Properties

Molecular Weight:  350.09
Volume:  338.293
LogP:  5.155
LogD:  2.746
LogS:  -4.863
# Rotatable Bonds:  10
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.442
Synthetic Accessibility Score:  3.282
Fsp3:  0.5
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:  -5.044
MDCK Permeability:  3.839446071651764e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.446
20% Bioavailability (F20%):  0.482
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  101.77436065673828%
Volume Distribution (VD):  0.431
Pgp-substrate:  0.7376300692558289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.42
CYP1A2-substrate:  0.26
CYP2C19-inhibitor:  0.915
CYP2C19-substrate:  0.325
CYP2C9-inhibitor:  0.89
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.38
CYP2D6-substrate:  0.897
CYP3A4-inhibitor:  0.716
CYP3A4-substrate:  0.039

ADMET: Excretion

Clearance (CL):  1.079
Half-life (T1/2):  0.822

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.873
Drug-inuced Liver Injury (DILI):  0.974
AMES Toxicity:  0.304
Rat Oral Acute Toxicity:  0.054
Maximum Recommended Daily Dose:  0.093
Skin Sensitization:  0.958
Carcinogencity:  0.438
Eye Corrosion:  0.952
Eye Irritation:  0.966
Respiratory Toxicity:  0.85

Download Data

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

  Natural Product: NPC45626

Natural Product ID:  NPC45626
Common Name*:   (9E,17E)-18-Bromooctadeca-9,17-Dien-5,7-Diynoic Acid
IUPAC Name:   (9E,17E)-18-bromooctadeca-9,17-dien-5,7-diynoic acid
Synonyms:  
Standard InCHIKey:  CJVPQXWIBONARO-UUUWWEMDSA-N
Standard InCHI:  InChI=1S/C18H23BrO2/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,3,5,7,9,11-14,16H2,(H,20,21)/b2-1+,17-15+
SMILES:  C(=CC#CC#CCCCC(=O)O)/CCCCCC/C=C/Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL449762
PubChem CID:   10089285
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 = 12000.0 nM PMID[547836]

☑ 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 NPC45626 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
0.9608 High Similarity NPC225066
0.9608 High Similarity NPC10081
0.9412 High Similarity NPC129458
0.9412 High Similarity NPC303765
0.9091 High Similarity NPC267817
0.8889 High Similarity NPC474672
0.8545 High Similarity NPC54766
0.8393 Intermediate Similarity NPC187777
0.8393 Intermediate Similarity NPC179764
0.8302 Intermediate Similarity NPC59051
0.8214 Intermediate Similarity NPC473863
0.8214 Intermediate Similarity NPC274290
0.8148 Intermediate Similarity NPC28205
0.8148 Intermediate Similarity NPC284212
0.8103 Intermediate Similarity NPC329819
0.8077 Intermediate Similarity NPC42304
0.8 Intermediate Similarity NPC92114
0.8 Intermediate Similarity NPC18357
0.7931 Intermediate Similarity NPC225929
0.7925 Intermediate Similarity NPC91495
0.7925 Intermediate Similarity NPC207292
0.7885 Intermediate Similarity NPC117572
0.7857 Intermediate Similarity NPC294548
0.7857 Intermediate Similarity NPC139029
0.7857 Intermediate Similarity NPC1813
0.7857 Intermediate Similarity NPC36061
0.7778 Intermediate Similarity NPC5413
0.7778 Intermediate Similarity NPC149821
0.7719 Intermediate Similarity NPC88966
0.7719 Intermediate Similarity NPC290563
0.7719 Intermediate Similarity NPC154245
0.7719 Intermediate Similarity NPC87564
0.7719 Intermediate Similarity NPC25417
0.7719 Intermediate Similarity NPC85813
0.7719 Intermediate Similarity NPC424
0.7719 Intermediate Similarity NPC6095
0.7719 Intermediate Similarity NPC261831
0.7719 Intermediate Similarity NPC32467
0.7719 Intermediate Similarity NPC281972
0.7679 Intermediate Similarity NPC281245
0.7586 Intermediate Similarity NPC477984
0.7544 Intermediate Similarity NPC321062
0.7544 Intermediate Similarity NPC70387
0.7541 Intermediate Similarity NPC235242
0.75 Intermediate Similarity NPC470412
0.75 Intermediate Similarity NPC470410
0.75 Intermediate Similarity NPC48162
0.7458 Intermediate Similarity NPC18951
0.7458 Intermediate Similarity NPC477201
0.7321 Intermediate Similarity NPC224227
0.7273 Intermediate Similarity NPC180534
0.7193 Intermediate Similarity NPC262968
0.7188 Intermediate Similarity NPC470320
0.7188 Intermediate Similarity NPC226592
0.717 Intermediate Similarity NPC270796
0.7167 Intermediate Similarity NPC325977
0.7119 Intermediate Similarity NPC137538
0.7119 Intermediate Similarity NPC322461
0.7097 Intermediate Similarity NPC106851
0.7097 Intermediate Similarity NPC274927
0.7069 Intermediate Similarity NPC161366
0.7 Intermediate Similarity NPC52264
0.6984 Remote Similarity NPC174447
0.6984 Remote Similarity NPC122521
0.6984 Remote Similarity NPC243532
0.6984 Remote Similarity NPC251042
0.6949 Remote Similarity NPC139545
0.6949 Remote Similarity NPC39633
0.6949 Remote Similarity NPC284224
0.6949 Remote Similarity NPC71761
0.6949 Remote Similarity NPC309606
0.6935 Remote Similarity NPC469373
0.6935 Remote Similarity NPC34416
0.6885 Remote Similarity NPC327388
0.6875 Remote Similarity NPC475984
0.6875 Remote Similarity NPC477829
0.6875 Remote Similarity NPC321838
0.6875 Remote Similarity NPC125312
0.6875 Remote Similarity NPC174560
0.6875 Remote Similarity NPC320305
0.6875 Remote Similarity NPC40082
0.6875 Remote Similarity NPC328776
0.6875 Remote Similarity NPC201939
0.6774 Remote Similarity NPC323597
0.6774 Remote Similarity NPC323498
0.6774 Remote Similarity NPC323436
0.6774 Remote Similarity NPC211752
0.6769 Remote Similarity NPC470965
0.6769 Remote Similarity NPC29697
0.6765 Remote Similarity NPC53302
0.6727 Remote Similarity NPC108195
0.6724 Remote Similarity NPC473768
0.6721 Remote Similarity NPC200845
0.6721 Remote Similarity NPC474513
0.6721 Remote Similarity NPC146551
0.6721 Remote Similarity NPC228473
0.6721 Remote Similarity NPC223677
0.6721 Remote Similarity NPC128061
0.6721 Remote Similarity NPC28779
0.6721 Remote Similarity NPC10316
0.6721 Remote Similarity NPC470963
0.6719 Remote Similarity NPC327112
0.6719 Remote Similarity NPC328311
0.6714 Remote Similarity NPC477983
0.6714 Remote Similarity NPC477981
0.6667 Remote Similarity NPC68343
0.6667 Remote Similarity NPC328089
0.6615 Remote Similarity NPC66460
0.6615 Remote Similarity NPC271282
0.6615 Remote Similarity NPC325929
0.6613 Remote Similarity NPC311648
0.6613 Remote Similarity NPC470964
0.661 Remote Similarity NPC129263
0.661 Remote Similarity NPC178586
0.661 Remote Similarity NPC470411
0.6567 Remote Similarity NPC476655
0.6567 Remote Similarity NPC136164
0.6567 Remote Similarity NPC318420
0.6567 Remote Similarity NPC245947
0.6567 Remote Similarity NPC476657
0.6567 Remote Similarity NPC255863
0.6567 Remote Similarity NPC326268
0.6567 Remote Similarity NPC476654
0.6562 Remote Similarity NPC329550
0.6562 Remote Similarity NPC329249
0.6557 Remote Similarity NPC87394
0.6552 Remote Similarity NPC475153
0.6552 Remote Similarity NPC207815
0.6508 Remote Similarity NPC48968
0.6508 Remote Similarity NPC594
0.65 Remote Similarity NPC473705
0.6481 Remote Similarity NPC103286
0.6481 Remote Similarity NPC163746
0.6471 Remote Similarity NPC476656
0.6471 Remote Similarity NPC476659
0.6471 Remote Similarity NPC477982
0.6462 Remote Similarity NPC81896
0.6462 Remote Similarity NPC321919
0.6452 Remote Similarity NPC152668
0.6441 Remote Similarity NPC474391
0.6393 Remote Similarity NPC34577
0.6393 Remote Similarity NPC26102
0.6393 Remote Similarity NPC477724
0.6393 Remote Similarity NPC187361
0.6379 Remote Similarity NPC216130
0.6377 Remote Similarity NPC22101
0.6377 Remote Similarity NPC148192
0.6377 Remote Similarity NPC99619
0.6377 Remote Similarity NPC127091
0.6377 Remote Similarity NPC104537
0.6377 Remote Similarity NPC26500
0.6377 Remote Similarity NPC330426
0.6377 Remote Similarity NPC271921
0.6364 Remote Similarity NPC71317
0.6364 Remote Similarity NPC149668
0.6364 Remote Similarity NPC301528
0.6364 Remote Similarity NPC113293
0.6364 Remote Similarity NPC129972
0.6351 Remote Similarity NPC470899
0.6346 Remote Similarity NPC158179
0.6333 Remote Similarity NPC151782
0.6333 Remote Similarity NPC477458
0.6316 Remote Similarity NPC474202
0.6316 Remote Similarity NPC276825
0.6316 Remote Similarity NPC474362
0.6308 Remote Similarity NPC473652
0.6308 Remote Similarity NPC474267
0.6308 Remote Similarity NPC329424
0.6308 Remote Similarity NPC322002
0.6308 Remote Similarity NPC222852
0.629 Remote Similarity NPC256209
0.629 Remote Similarity NPC269615
0.629 Remote Similarity NPC49059
0.629 Remote Similarity NPC473532
0.629 Remote Similarity NPC300121
0.6286 Remote Similarity NPC476614
0.6286 Remote Similarity NPC477980
0.6286 Remote Similarity NPC324981
0.6286 Remote Similarity NPC273508
0.6286 Remote Similarity NPC473559
0.6286 Remote Similarity NPC141481
0.6286 Remote Similarity NPC209327
0.6286 Remote Similarity NPC48218
0.6271 Remote Similarity NPC163345
0.6271 Remote Similarity NPC302310
0.6269 Remote Similarity NPC322457
0.625 Remote Similarity NPC193975
0.625 Remote Similarity NPC281230
0.625 Remote Similarity NPC255837
0.625 Remote Similarity NPC19305
0.625 Remote Similarity NPC212730
0.625 Remote Similarity NPC265551
0.625 Remote Similarity NPC472445
0.625 Remote Similarity NPC44542
0.623 Remote Similarity NPC236872
0.623 Remote Similarity NPC477779
0.6212 Remote Similarity NPC299730
0.6212 Remote Similarity NPC471278
0.6212 Remote Similarity NPC143857
0.6212 Remote Similarity NPC229252

  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 NPC45626 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
0.7885 Intermediate Similarity NPD4222 Approved
0.7857 Intermediate Similarity NPD3172 Approved
0.7778 Intermediate Similarity NPD3173 Approved
0.7719 Intermediate Similarity NPD3194 Approved
0.7719 Intermediate Similarity NPD3195 Phase 2
0.7719 Intermediate Similarity NPD4266 Approved
0.7719 Intermediate Similarity NPD3196 Approved
0.7547 Intermediate Similarity NPD39 Approved
0.7273 Intermediate Similarity NPD622 Approved
0.7222 Intermediate Similarity NPD3174 Discontinued
0.7193 Intermediate Similarity NPD29 Approved
0.7193 Intermediate Similarity NPD28 Approved
0.717 Intermediate Similarity NPD5326 Phase 3
0.6719 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6667 Remote Similarity NPD3197 Phase 1
0.6667 Remote Similarity NPD5343 Approved
0.6154 Remote Similarity NPD6109 Phase 1
0.614 Remote Similarity NPD6097 Approved
0.614 Remote Similarity NPD6096 Approved
0.5915 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5802 Remote Similarity NPD5331 Approved
0.5802 Remote Similarity NPD5332 Approved
0.5738 Remote Similarity NPD4220 Pre-registration
0.5692 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5614 Remote Similarity NPD2270 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