Structure

Physi-Chem Properties

Molecular Weight:  350.09
Volume:  338.293
LogP:  4.621
LogD:  2.328
LogS:  -4.401
# Rotatable Bonds:  9
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  3.309
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:  -4.636
MDCK Permeability:  4.959396756021306e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.04
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  101.09880828857422%
Volume Distribution (VD):  0.48
Pgp-substrate:  0.5682588219642639%

ADMET: Metabolism

CYP1A2-inhibitor:  0.454
CYP1A2-substrate:  0.23
CYP2C19-inhibitor:  0.914
CYP2C19-substrate:  0.604
CYP2C9-inhibitor:  0.869
CYP2C9-substrate:  0.999
CYP2D6-inhibitor:  0.857
CYP2D6-substrate:  0.916
CYP3A4-inhibitor:  0.843
CYP3A4-substrate:  0.063

ADMET: Excretion

Clearance (CL):  1.125
Half-life (T1/2):  0.746

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.959
Drug-inuced Liver Injury (DILI):  0.976
AMES Toxicity:  0.691
Rat Oral Acute Toxicity:  0.066
Maximum Recommended Daily Dose:  0.04
Skin Sensitization:  0.956
Carcinogencity:  0.658
Eye Corrosion:  0.946
Eye Irritation:  0.959
Respiratory Toxicity:  0.952

Download Data

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

  Natural Product: NPC267817

Natural Product ID:  NPC267817
Common Name*:   18-Bromooctadeca-(9E,17E)-Diene-7,15-Diynoic Acid
IUPAC Name:   (9E,17E)-18-bromooctadeca-9,17-dien-7,15-diynoic acid
Synonyms:  
Standard InCHIKey:  PKRHWWLSHFMWNA-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,3,5,7-10,12,14,16H2,(H,20,21)/b2-1+,17-15+
SMILES:  Br/C=C/C#CCCCC/C=C/C#CCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL481648
PubChem CID:   9543590
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
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10543913]
NPO24512 Xestospongia testudinaria 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
NPT1315 Individual Protein Adenosine A1 receptor Rattus norvegicus IC50 = 106000.0 nM PMID[528411]

☑ 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 NPC267817 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
0.9091 High Similarity NPC274290
0.9091 High Similarity NPC45626
0.9091 High Similarity NPC473863
0.9091 High Similarity NPC54766
0.9074 High Similarity NPC225066
0.9074 High Similarity NPC10081
0.8929 High Similarity NPC187777
0.8929 High Similarity NPC179764
0.8889 High Similarity NPC303765
0.8889 High Similarity NPC129458
0.8545 High Similarity NPC18357
0.8448 Intermediate Similarity NPC225929
0.8393 Intermediate Similarity NPC1813
0.8393 Intermediate Similarity NPC321062
0.8393 Intermediate Similarity NPC36061
0.8393 Intermediate Similarity NPC139029
0.8393 Intermediate Similarity NPC70387
0.8393 Intermediate Similarity NPC294548
0.8364 Intermediate Similarity NPC28205
0.8364 Intermediate Similarity NPC284212
0.8246 Intermediate Similarity NPC88966
0.8246 Intermediate Similarity NPC424
0.8246 Intermediate Similarity NPC32467
0.8246 Intermediate Similarity NPC87564
0.8246 Intermediate Similarity NPC85813
0.8246 Intermediate Similarity NPC290563
0.8246 Intermediate Similarity NPC261831
0.8246 Intermediate Similarity NPC6095
0.8246 Intermediate Similarity NPC25417
0.8246 Intermediate Similarity NPC281972
0.8246 Intermediate Similarity NPC154245
0.8214 Intermediate Similarity NPC281245
0.8148 Intermediate Similarity NPC207292
0.8103 Intermediate Similarity NPC474672
0.8036 Intermediate Similarity NPC470412
0.8036 Intermediate Similarity NPC470410
0.8033 Intermediate Similarity NPC235242
0.8 Intermediate Similarity NPC149821
0.8 Intermediate Similarity NPC5413
0.7966 Intermediate Similarity NPC18951
0.7966 Intermediate Similarity NPC477201
0.7895 Intermediate Similarity NPC92114
0.7857 Intermediate Similarity NPC224227
0.7818 Intermediate Similarity NPC180534
0.7719 Intermediate Similarity NPC262968
0.7656 Intermediate Similarity NPC470320
0.7656 Intermediate Similarity NPC226592
0.7636 Intermediate Similarity NPC42304
0.7619 Intermediate Similarity NPC477829
0.7586 Intermediate Similarity NPC161366
0.7581 Intermediate Similarity NPC274927
0.7581 Intermediate Similarity NPC106851
0.7544 Intermediate Similarity NPC59051
0.75 Intermediate Similarity NPC91495
0.746 Intermediate Similarity NPC251042
0.746 Intermediate Similarity NPC174447
0.746 Intermediate Similarity NPC122521
0.746 Intermediate Similarity NPC243532
0.7458 Intermediate Similarity NPC39633
0.7458 Intermediate Similarity NPC71761
0.7458 Intermediate Similarity NPC309606
0.7458 Intermediate Similarity NPC139545
0.7455 Intermediate Similarity NPC117572
0.7419 Intermediate Similarity NPC329819
0.7419 Intermediate Similarity NPC34416
0.7344 Intermediate Similarity NPC125312
0.7344 Intermediate Similarity NPC40082
0.7344 Intermediate Similarity NPC201939
0.7344 Intermediate Similarity NPC174560
0.7213 Intermediate Similarity NPC28779
0.7213 Intermediate Similarity NPC228473
0.7213 Intermediate Similarity NPC223677
0.7213 Intermediate Similarity NPC128061
0.7213 Intermediate Similarity NPC200845
0.7213 Intermediate Similarity NPC10316
0.7206 Intermediate Similarity NPC53302
0.7121 Intermediate Similarity NPC68343
0.7121 Intermediate Similarity NPC328089
0.7119 Intermediate Similarity NPC48162
0.7097 Intermediate Similarity NPC325977
0.7049 Intermediate Similarity NPC87394
0.7015 Intermediate Similarity NPC245947
0.7015 Intermediate Similarity NPC255863
0.7015 Intermediate Similarity NPC318420
0.7015 Intermediate Similarity NPC136164
0.7015 Intermediate Similarity NPC326268
0.6935 Remote Similarity NPC477984
0.6935 Remote Similarity NPC52264
0.6897 Remote Similarity NPC216130
0.6875 Remote Similarity NPC469373
0.6833 Remote Similarity NPC470411
0.6818 Remote Similarity NPC320305
0.6818 Remote Similarity NPC328776
0.6818 Remote Similarity NPC475984
0.6818 Remote Similarity NPC321838
0.6812 Remote Similarity NPC330426
0.6812 Remote Similarity NPC271921
0.6812 Remote Similarity NPC22101
0.6812 Remote Similarity NPC148192
0.6812 Remote Similarity NPC104537
0.6812 Remote Similarity NPC99619
0.6812 Remote Similarity NPC26500
0.6812 Remote Similarity NPC127091
0.6786 Remote Similarity NPC19305
0.6786 Remote Similarity NPC255837
0.6786 Remote Similarity NPC270796
0.6774 Remote Similarity NPC322461
0.6774 Remote Similarity NPC137538
0.6769 Remote Similarity NPC329550
0.6716 Remote Similarity NPC470965
0.6716 Remote Similarity NPC29697
0.6714 Remote Similarity NPC473559
0.6714 Remote Similarity NPC476614
0.6714 Remote Similarity NPC324981
0.6714 Remote Similarity NPC48218
0.6714 Remote Similarity NPC141481
0.6667 Remote Similarity NPC229252
0.6667 Remote Similarity NPC327112
0.6667 Remote Similarity NPC8219
0.6667 Remote Similarity NPC142423
0.6667 Remote Similarity NPC328311
0.6667 Remote Similarity NPC143857
0.6667 Remote Similarity NPC308294
0.662 Remote Similarity NPC143396
0.662 Remote Similarity NPC317583
0.6618 Remote Similarity NPC234767
0.6613 Remote Similarity NPC284224
0.6579 Remote Similarity NPC469495
0.6571 Remote Similarity NPC60120
0.6571 Remote Similarity NPC475443
0.6571 Remote Similarity NPC473829
0.6567 Remote Similarity NPC66460
0.6567 Remote Similarity NPC271282
0.6567 Remote Similarity NPC325929
0.6562 Remote Similarity NPC327388
0.6557 Remote Similarity NPC129263
0.6528 Remote Similarity NPC476660
0.6528 Remote Similarity NPC42526
0.65 Remote Similarity NPC207815
0.65 Remote Similarity NPC163345
0.6494 Remote Similarity NPC209995
0.6471 Remote Similarity NPC54925
0.6471 Remote Similarity NPC477707
0.6462 Remote Similarity NPC323498
0.6462 Remote Similarity NPC323436
0.6462 Remote Similarity NPC323597
0.6462 Remote Similarity NPC211752
0.6429 Remote Similarity NPC163746
0.6429 Remote Similarity NPC103286
0.641 Remote Similarity NPC200446
0.6393 Remote Similarity NPC474391
0.6393 Remote Similarity NPC473768
0.6389 Remote Similarity NPC473772
0.6351 Remote Similarity NPC325627
0.6349 Remote Similarity NPC26102
0.6349 Remote Similarity NPC477724
0.6349 Remote Similarity NPC34577
0.6349 Remote Similarity NPC187361
0.6324 Remote Similarity NPC113293
0.6316 Remote Similarity NPC71317
0.6316 Remote Similarity NPC129972
0.6316 Remote Similarity NPC301528
0.6301 Remote Similarity NPC67183
0.629 Remote Similarity NPC477458
0.629 Remote Similarity NPC178586
0.6286 Remote Similarity NPC317881
0.6286 Remote Similarity NPC320642
0.6286 Remote Similarity NPC323477
0.6286 Remote Similarity NPC323045
0.6269 Remote Similarity NPC329249
0.6269 Remote Similarity NPC473652
0.6269 Remote Similarity NPC474267
0.6267 Remote Similarity NPC476046
0.6267 Remote Similarity NPC227396
0.6267 Remote Similarity NPC92558
0.6267 Remote Similarity NPC241854
0.6267 Remote Similarity NPC3753
0.6267 Remote Similarity NPC283908
0.6267 Remote Similarity NPC103958
0.6267 Remote Similarity NPC183503
0.6267 Remote Similarity NPC251970
0.6267 Remote Similarity NPC474321
0.6267 Remote Similarity NPC55527
0.6267 Remote Similarity NPC161923
0.6267 Remote Similarity NPC237591
0.625 Remote Similarity NPC256209
0.625 Remote Similarity NPC49059
0.6232 Remote Similarity NPC477830
0.623 Remote Similarity NPC304162
0.6216 Remote Similarity NPC160817
0.6216 Remote Similarity NPC477981
0.6216 Remote Similarity NPC477983
0.6216 Remote Similarity NPC186531
0.6216 Remote Similarity NPC288667
0.6216 Remote Similarity NPC320669
0.6216 Remote Similarity NPC320119
0.6216 Remote Similarity NPC318814
0.6212 Remote Similarity NPC281230
0.6197 Remote Similarity NPC328653
0.6197 Remote Similarity NPC322035

  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 NPC267817 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
0.8393 Intermediate Similarity NPD3172 Approved
0.8246 Intermediate Similarity NPD4266 Approved
0.8246 Intermediate Similarity NPD3196 Approved
0.8246 Intermediate Similarity NPD3194 Approved
0.8246 Intermediate Similarity NPD3195 Phase 2
0.8 Intermediate Similarity NPD3173 Approved
0.7818 Intermediate Similarity NPD622 Approved
0.7719 Intermediate Similarity NPD28 Approved
0.7719 Intermediate Similarity NPD29 Approved
0.7455 Intermediate Similarity NPD4222 Approved
0.7455 Intermediate Similarity NPD3174 Discontinued
0.7143 Intermediate Similarity NPD39 Approved
0.7121 Intermediate Similarity NPD3197 Phase 1
0.6786 Remote Similarity NPD5326 Phase 3
0.6667 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6333 Remote Similarity NPD5343 Approved
0.614 Remote Similarity NPD2270 Approved
0.6111 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6071 Remote Similarity NPD9655 Approved
0.6071 Remote Similarity NPD633 Phase 3
0.6071 Remote Similarity NPD9448 Phase 2
0.6 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5972 Remote Similarity NPD7331 Phase 2
0.5949 Remote Similarity NPD3732 Approved
0.5882 Remote Similarity NPD6109 Phase 1
0.5833 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6096 Approved
0.5833 Remote Similarity NPD6097 Approved
0.5823 Remote Similarity NPD4756 Discovery
0.5802 Remote Similarity NPD5368 Approved
0.5783 Remote Similarity NPD5331 Approved
0.5783 Remote Similarity NPD5332 Approved
0.575 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5732 Remote Similarity NPD5369 Approved
0.5672 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5663 Remote Similarity NPD6435 Approved
0.5663 Remote Similarity NPD4269 Approved
0.5663 Remote Similarity NPD4270 Approved
0.5614 Remote Similarity NPD3206 Approved
0.561 Remote Similarity NPD4252 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