Structure

Physi-Chem Properties

Molecular Weight:  346.06
Volume:  333.02
LogP:  4.531
LogD:  2.302
LogS:  -4.726
# Rotatable Bonds:  8
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.526
Synthetic Accessibility Score:  3.674
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:  -4.581
MDCK Permeability:  4.918277045362629e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.349
20% Bioavailability (F20%):  0.05
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.5383071899414%
Volume Distribution (VD):  0.457
Pgp-substrate:  1.1112631559371948%

ADMET: Metabolism

CYP1A2-inhibitor:  0.537
CYP1A2-substrate:  0.199
CYP2C19-inhibitor:  0.907
CYP2C19-substrate:  0.305
CYP2C9-inhibitor:  0.901
CYP2C9-substrate:  0.999
CYP2D6-inhibitor:  0.798
CYP2D6-substrate:  0.91
CYP3A4-inhibitor:  0.778
CYP3A4-substrate:  0.06

ADMET: Excretion

Clearance (CL):  0.874
Half-life (T1/2):  0.691

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.903
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.586
Rat Oral Acute Toxicity:  0.097
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.966
Carcinogencity:  0.442
Eye Corrosion:  0.978
Eye Irritation:  0.976
Respiratory Toxicity:  0.955

Download Data

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

  Natural Product: NPC129458

Natural Product ID:  NPC129458
Common Name*:   (9E,15E)-18-Bromooctadeca-9,15-Dien-5,7,17-Triynoic Acid
IUPAC Name:   (9E,15E)-18-bromooctadeca-9,15-dien-5,7,17-triynoic acid
Synonyms:  
Standard InCHIKey:  QEUOZGGZDVOBGG-JKWAYVKBSA-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/h1-2,11,13H,3,5,7,9,12,14,16H2,(H,20,21)/b2-1+,13-11+
SMILES:  C(=CC#CC#CCCCC(=O)O)/CCCC/C=C/C#CBr
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL478973
PubChem CID:   10089023
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 = 7000.0 nM PMID[550813]

☑ 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 NPC129458 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
0.9796 High Similarity NPC225066
0.9796 High Similarity NPC10081
0.9592 High Similarity NPC303765
0.9412 High Similarity NPC45626
0.8889 High Similarity NPC267817
0.8627 High Similarity NPC28205
0.8627 High Similarity NPC284212
0.8571 High Similarity NPC42304
0.84 Intermediate Similarity NPC91495
0.84 Intermediate Similarity NPC207292
0.8367 Intermediate Similarity NPC117572
0.8333 Intermediate Similarity NPC54766
0.8333 Intermediate Similarity NPC474672
0.8333 Intermediate Similarity NPC274290
0.8333 Intermediate Similarity NPC473863
0.8235 Intermediate Similarity NPC5413
0.8235 Intermediate Similarity NPC149821
0.8182 Intermediate Similarity NPC179764
0.8182 Intermediate Similarity NPC187777
0.8077 Intermediate Similarity NPC59051
0.7925 Intermediate Similarity NPC48162
0.7895 Intermediate Similarity NPC329819
0.7778 Intermediate Similarity NPC18357
0.7778 Intermediate Similarity NPC92114
0.7719 Intermediate Similarity NPC225929
0.7636 Intermediate Similarity NPC321062
0.7636 Intermediate Similarity NPC294548
0.7636 Intermediate Similarity NPC1813
0.7636 Intermediate Similarity NPC36061
0.7636 Intermediate Similarity NPC70387
0.7636 Intermediate Similarity NPC139029
0.76 Intermediate Similarity NPC270796
0.75 Intermediate Similarity NPC281972
0.75 Intermediate Similarity NPC290563
0.75 Intermediate Similarity NPC85813
0.75 Intermediate Similarity NPC424
0.75 Intermediate Similarity NPC25417
0.75 Intermediate Similarity NPC32467
0.75 Intermediate Similarity NPC88966
0.75 Intermediate Similarity NPC322461
0.75 Intermediate Similarity NPC87564
0.75 Intermediate Similarity NPC6095
0.75 Intermediate Similarity NPC261831
0.75 Intermediate Similarity NPC154245
0.7455 Intermediate Similarity NPC281245
0.7368 Intermediate Similarity NPC477984
0.7333 Intermediate Similarity NPC235242
0.7273 Intermediate Similarity NPC470412
0.7273 Intermediate Similarity NPC470410
0.7241 Intermediate Similarity NPC18951
0.7241 Intermediate Similarity NPC325977
0.7241 Intermediate Similarity NPC477201
0.7241 Intermediate Similarity NPC327388
0.7119 Intermediate Similarity NPC323597
0.7119 Intermediate Similarity NPC323498
0.7119 Intermediate Similarity NPC323436
0.7119 Intermediate Similarity NPC211752
0.7091 Intermediate Similarity NPC224227
0.7037 Intermediate Similarity NPC180534
0.7018 Intermediate Similarity NPC284224
0.6984 Remote Similarity NPC226592
0.6984 Remote Similarity NPC470320
0.6964 Remote Similarity NPC178586
0.6964 Remote Similarity NPC470411
0.6964 Remote Similarity NPC262968
0.6935 Remote Similarity NPC477829
0.6897 Remote Similarity NPC137538
0.6885 Remote Similarity NPC106851
0.6885 Remote Similarity NPC274927
0.6885 Remote Similarity NPC329550
0.6885 Remote Similarity NPC329249
0.6842 Remote Similarity NPC161366
0.6786 Remote Similarity NPC473768
0.678 Remote Similarity NPC52264
0.6774 Remote Similarity NPC174447
0.6774 Remote Similarity NPC251042
0.6774 Remote Similarity NPC328311
0.6774 Remote Similarity NPC81896
0.6774 Remote Similarity NPC321919
0.6774 Remote Similarity NPC122521
0.6774 Remote Similarity NPC327112
0.6774 Remote Similarity NPC243532
0.6735 Remote Similarity NPC158179
0.6724 Remote Similarity NPC139545
0.6724 Remote Similarity NPC71761
0.6724 Remote Similarity NPC39633
0.6724 Remote Similarity NPC309606
0.6721 Remote Similarity NPC469373
0.6721 Remote Similarity NPC34416
0.6667 Remote Similarity NPC328776
0.6667 Remote Similarity NPC125312
0.6667 Remote Similarity NPC174560
0.6667 Remote Similarity NPC475984
0.6667 Remote Similarity NPC320305
0.6667 Remote Similarity NPC321838
0.6667 Remote Similarity NPC201939
0.6667 Remote Similarity NPC40082
0.6613 Remote Similarity NPC322002
0.661 Remote Similarity NPC300121
0.6607 Remote Similarity NPC163345
0.6567 Remote Similarity NPC53302
0.6562 Remote Similarity NPC29697
0.6562 Remote Similarity NPC470965
0.6562 Remote Similarity NPC322457
0.6557 Remote Similarity NPC472445
0.6552 Remote Similarity NPC477779
0.6522 Remote Similarity NPC477983
0.6522 Remote Similarity NPC477981
0.65 Remote Similarity NPC146551
0.65 Remote Similarity NPC28779
0.65 Remote Similarity NPC152668
0.65 Remote Similarity NPC228473
0.65 Remote Similarity NPC474513
0.65 Remote Similarity NPC67367
0.65 Remote Similarity NPC470963
0.65 Remote Similarity NPC200845
0.65 Remote Similarity NPC10316
0.65 Remote Similarity NPC223677
0.65 Remote Similarity NPC128061
0.6481 Remote Similarity NPC108195
0.6462 Remote Similarity NPC68343
0.6462 Remote Similarity NPC328089
0.6406 Remote Similarity NPC66460
0.6406 Remote Similarity NPC113293
0.6406 Remote Similarity NPC271282
0.6406 Remote Similarity NPC325929
0.6393 Remote Similarity NPC470964
0.6393 Remote Similarity NPC311648
0.6379 Remote Similarity NPC129263
0.6379 Remote Similarity NPC477777
0.6364 Remote Similarity NPC136164
0.6364 Remote Similarity NPC317881
0.6364 Remote Similarity NPC276825
0.6364 Remote Similarity NPC323045
0.6364 Remote Similarity NPC245947
0.6364 Remote Similarity NPC320642
0.6364 Remote Similarity NPC318420
0.6364 Remote Similarity NPC476655
0.6364 Remote Similarity NPC474202
0.6364 Remote Similarity NPC323477
0.6364 Remote Similarity NPC255863
0.6364 Remote Similarity NPC326268
0.6364 Remote Similarity NPC474362
0.6364 Remote Similarity NPC476657
0.6364 Remote Similarity NPC476654
0.6349 Remote Similarity NPC222852
0.6349 Remote Similarity NPC318306
0.6346 Remote Similarity NPC27444
0.6346 Remote Similarity NPC329762
0.6346 Remote Similarity NPC103236
0.6333 Remote Similarity NPC87394
0.6316 Remote Similarity NPC302310
0.6316 Remote Similarity NPC207815
0.629 Remote Similarity NPC212730
0.629 Remote Similarity NPC594
0.629 Remote Similarity NPC265551
0.629 Remote Similarity NPC44542
0.629 Remote Similarity NPC48968
0.6275 Remote Similarity NPC155880
0.6275 Remote Similarity NPC92863
0.6275 Remote Similarity NPC73245
0.6271 Remote Similarity NPC216407
0.6271 Remote Similarity NPC473705
0.6269 Remote Similarity NPC477982
0.6269 Remote Similarity NPC476659
0.6269 Remote Similarity NPC476656
0.6269 Remote Similarity NPC328653
0.625 Remote Similarity NPC157096
0.6226 Remote Similarity NPC163746
0.6226 Remote Similarity NPC103286
0.6207 Remote Similarity NPC474391
0.6207 Remote Similarity NPC473487
0.619 Remote Similarity NPC325734
0.6176 Remote Similarity NPC478097
0.6176 Remote Similarity NPC22101
0.6176 Remote Similarity NPC330426
0.6176 Remote Similarity NPC478100
0.6176 Remote Similarity NPC99619
0.6176 Remote Similarity NPC49863
0.6176 Remote Similarity NPC148192
0.6176 Remote Similarity NPC127091
0.6176 Remote Similarity NPC271921
0.6176 Remote Similarity NPC104537
0.6176 Remote Similarity NPC26500
0.6167 Remote Similarity NPC217188
0.6167 Remote Similarity NPC477724
0.6167 Remote Similarity NPC26102
0.6167 Remote Similarity NPC187361
0.6167 Remote Similarity NPC61177
0.6167 Remote Similarity NPC34577
0.6164 Remote Similarity NPC470899
0.614 Remote Similarity NPC216130
0.6129 Remote Similarity NPC324224
0.6129 Remote Similarity NPC472808
0.6119 Remote Similarity NPC478098
0.6119 Remote Similarity NPC478099
0.6111 Remote Similarity NPC301528
0.6111 Remote Similarity NPC149668
0.6111 Remote Similarity NPC71317
0.6111 Remote Similarity NPC129972

  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 NPC129458 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
0.8367 Intermediate Similarity NPD4222 Approved
0.8235 Intermediate Similarity NPD3173 Approved
0.8 Intermediate Similarity NPD39 Approved
0.7647 Intermediate Similarity NPD3174 Discontinued
0.7636 Intermediate Similarity NPD3172 Approved
0.76 Intermediate Similarity NPD5326 Phase 3
0.75 Intermediate Similarity NPD3196 Approved
0.75 Intermediate Similarity NPD4266 Approved
0.75 Intermediate Similarity NPD3195 Phase 2
0.75 Intermediate Similarity NPD3194 Approved
0.7037 Intermediate Similarity NPD5343 Approved
0.7037 Intermediate Similarity NPD622 Approved
0.6964 Remote Similarity NPD29 Approved
0.6964 Remote Similarity NPD28 Approved
0.6774 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6481 Remote Similarity NPD6097 Approved
0.6481 Remote Similarity NPD6096 Approved
0.6462 Remote Similarity NPD3197 Phase 1
0.6452 Remote Similarity NPD6109 Phase 1
0.6176 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6034 Remote Similarity NPD4220 Pre-registration
0.5833 Remote Similarity NPD6927 Phase 3
0.5741 Remote Similarity NPD9635 Discontinued
0.5625 Remote Similarity NPD5332 Approved
0.5625 Remote Similarity NPD5331 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