Structure

Physi-Chem Properties

Molecular Weight:  230.13
Volume:  267.121
LogP:  4.305
LogD:  2.387
LogS:  -4.2
# Rotatable Bonds:  6
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.562
Synthetic Accessibility Score:  2.983
Fsp3:  0.533
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:  -4.882
MDCK Permeability:  7.887134415796027e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.56
20% Bioavailability (F20%):  0.246
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  102.15580749511719%
Volume Distribution (VD):  0.426
Pgp-substrate:  1.3442918062210083%

ADMET: Metabolism

CYP1A2-inhibitor:  0.519
CYP1A2-substrate:  0.184
CYP2C19-inhibitor:  0.843
CYP2C19-substrate:  0.389
CYP2C9-inhibitor:  0.833
CYP2C9-substrate:  0.994
CYP2D6-inhibitor:  0.024
CYP2D6-substrate:  0.513
CYP3A4-inhibitor:  0.359
CYP3A4-substrate:  0.032

ADMET: Excretion

Clearance (CL):  3.212
Half-life (T1/2):  0.786

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.204
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.583
Rat Oral Acute Toxicity:  0.106
Maximum Recommended Daily Dose:  0.037
Skin Sensitization:  0.956
Carcinogencity:  0.469
Eye Corrosion:  0.988
Eye Irritation:  0.979
Respiratory Toxicity:  0.782

Download Data

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

  Natural Product: NPC73245

Natural Product ID:  NPC73245
Common Name*:   Pentadeca-6,8,10-Triynoic Acid
IUPAC Name:   pentadeca-6,8,10-triynoic acid
Synonyms:   Pentadeca-6,8,10-Triynoic Acid
Standard InCHIKey:  ZRUBGTBVDWZJCR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H18O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15(16)17/h2-4,11-14H2,1H3,(H,16,17)
SMILES:  CCCCC#CC#CC#CCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL447088
PubChem CID:   10633230
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
NPO32503 heisteria acuminata Species Erythropalaceae Eukaryota bark n.a. n.a. PMID[9584394]

☑ 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
NPT2 Others Unspecified Inhibition = 55.0 % PMID[469310]
NPT2 Others Unspecified Inhibition = 36.0 % PMID[469310]
NPT2 Others Unspecified Inhibition = 18.0 % PMID[469310]

☑ 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 NPC73245 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
0.9211 High Similarity NPC103286
0.9211 High Similarity NPC163746
0.9167 High Similarity NPC158179
0.8974 High Similarity NPC71317
0.8974 High Similarity NPC129972
0.8974 High Similarity NPC301528
0.875 High Similarity NPC255837
0.875 High Similarity NPC19305
0.8571 High Similarity NPC175342
0.8537 High Similarity NPC8219
0.8205 Intermediate Similarity NPC201844
0.8205 Intermediate Similarity NPC113928
0.8205 Intermediate Similarity NPC301696
0.8205 Intermediate Similarity NPC14227
0.8205 Intermediate Similarity NPC261080
0.8205 Intermediate Similarity NPC154186
0.8205 Intermediate Similarity NPC279026
0.8205 Intermediate Similarity NPC301585
0.8056 Intermediate Similarity NPC18224
0.8056 Intermediate Similarity NPC328710
0.7895 Intermediate Similarity NPC155263
0.7805 Intermediate Similarity NPC149184
0.7805 Intermediate Similarity NPC196924
0.7805 Intermediate Similarity NPC216630
0.7805 Intermediate Similarity NPC209970
0.7805 Intermediate Similarity NPC171736
0.7805 Intermediate Similarity NPC325452
0.7805 Intermediate Similarity NPC248763
0.7805 Intermediate Similarity NPC307783
0.7778 Intermediate Similarity NPC304162
0.775 Intermediate Similarity NPC183424
0.775 Intermediate Similarity NPC294085
0.775 Intermediate Similarity NPC214610
0.775 Intermediate Similarity NPC118968
0.7714 Intermediate Similarity NPC174368
0.7692 Intermediate Similarity NPC252843
0.7692 Intermediate Similarity NPC109026
0.7632 Intermediate Similarity NPC317203
0.7619 Intermediate Similarity NPC67462
0.75 Intermediate Similarity NPC268826
0.7447 Intermediate Similarity NPC470411
0.7447 Intermediate Similarity NPC28205
0.7447 Intermediate Similarity NPC284212
0.7447 Intermediate Similarity NPC470412
0.7447 Intermediate Similarity NPC470410
0.7442 Intermediate Similarity NPC74845
0.7436 Intermediate Similarity NPC154642
0.7436 Intermediate Similarity NPC134782
0.7436 Intermediate Similarity NPC80396
0.7368 Intermediate Similarity NPC57499
0.7317 Intermediate Similarity NPC3531
0.7273 Intermediate Similarity NPC55023
0.7179 Intermediate Similarity NPC156630
0.7111 Intermediate Similarity NPC314679
0.7111 Intermediate Similarity NPC30195
0.7111 Intermediate Similarity NPC12438
0.7083 Intermediate Similarity NPC100096
0.7073 Intermediate Similarity NPC305660
0.7073 Intermediate Similarity NPC22903
0.7073 Intermediate Similarity NPC54980
0.7073 Intermediate Similarity NPC201622
0.6957 Remote Similarity NPC42304
0.6957 Remote Similarity NPC21844
0.6957 Remote Similarity NPC324004
0.6957 Remote Similarity NPC328497
0.6939 Remote Similarity NPC18357
0.6923 Remote Similarity NPC127142
0.6923 Remote Similarity NPC154396
0.6923 Remote Similarity NPC7814
0.6905 Remote Similarity NPC31551
0.6905 Remote Similarity NPC81263
0.6905 Remote Similarity NPC219536
0.6905 Remote Similarity NPC80234
0.6863 Remote Similarity NPC473863
0.6863 Remote Similarity NPC274290
0.6857 Remote Similarity NPC149209
0.6818 Remote Similarity NPC289686
0.6809 Remote Similarity NPC477878
0.6809 Remote Similarity NPC324793
0.6809 Remote Similarity NPC200618
0.6809 Remote Similarity NPC131770
0.6809 Remote Similarity NPC106872
0.6744 Remote Similarity NPC28598
0.6744 Remote Similarity NPC250028
0.6744 Remote Similarity NPC12156
0.6744 Remote Similarity NPC40597
0.6744 Remote Similarity NPC161097
0.6744 Remote Similarity NPC149299
0.6744 Remote Similarity NPC256163
0.6731 Remote Similarity NPC187777
0.6731 Remote Similarity NPC179764
0.6667 Remote Similarity NPC125575
0.6667 Remote Similarity NPC149821
0.6667 Remote Similarity NPC5413
0.6667 Remote Similarity NPC286695
0.6667 Remote Similarity NPC322892
0.6591 Remote Similarity NPC53541
0.6585 Remote Similarity NPC80641
0.6538 Remote Similarity NPC54766
0.6531 Remote Similarity NPC90904
0.6512 Remote Similarity NPC223249
0.6458 Remote Similarity NPC207292
0.6458 Remote Similarity NPC180534
0.6444 Remote Similarity NPC203531
0.6444 Remote Similarity NPC236579
0.6429 Remote Similarity NPC206924
0.6429 Remote Similarity NPC14608
0.641 Remote Similarity NPC40965
0.641 Remote Similarity NPC280532
0.641 Remote Similarity NPC12904
0.6383 Remote Similarity NPC166287
0.6364 Remote Similarity NPC165533
0.6341 Remote Similarity NPC155872
0.6341 Remote Similarity NPC289344
0.6327 Remote Similarity NPC26253
0.6316 Remote Similarity NPC151140
0.6316 Remote Similarity NPC104195
0.6316 Remote Similarity NPC61066
0.6316 Remote Similarity NPC122768
0.6304 Remote Similarity NPC76051
0.6304 Remote Similarity NPC323974
0.6304 Remote Similarity NPC317128
0.6296 Remote Similarity NPC225929
0.6279 Remote Similarity NPC38930
0.6279 Remote Similarity NPC325454
0.6275 Remote Similarity NPC161366
0.6275 Remote Similarity NPC281245
0.6275 Remote Similarity NPC129458
0.6275 Remote Similarity NPC92114
0.6222 Remote Similarity NPC474361
0.62 Remote Similarity NPC50457
0.6182 Remote Similarity NPC267817
0.617 Remote Similarity NPC47363
0.617 Remote Similarity NPC469781
0.617 Remote Similarity NPC287231
0.6154 Remote Similarity NPC139029
0.6154 Remote Similarity NPC72722
0.6154 Remote Similarity NPC1813
0.6154 Remote Similarity NPC294548
0.6154 Remote Similarity NPC321062
0.6154 Remote Similarity NPC225066
0.6154 Remote Similarity NPC10081
0.6154 Remote Similarity NPC36061
0.6154 Remote Similarity NPC70387
0.6136 Remote Similarity NPC94368
0.6122 Remote Similarity NPC91495
0.6098 Remote Similarity NPC286498
0.6047 Remote Similarity NPC317945
0.6042 Remote Similarity NPC52700
0.6042 Remote Similarity NPC145045
0.6042 Remote Similarity NPC105329
0.6042 Remote Similarity NPC117572
0.6042 Remote Similarity NPC63182
0.6042 Remote Similarity NPC308301
0.6042 Remote Similarity NPC172042
0.6038 Remote Similarity NPC25417
0.6038 Remote Similarity NPC23155
0.6038 Remote Similarity NPC424
0.6038 Remote Similarity NPC6095
0.6038 Remote Similarity NPC87394
0.6038 Remote Similarity NPC154245
0.6038 Remote Similarity NPC469937
0.6038 Remote Similarity NPC53463
0.6038 Remote Similarity NPC87564
0.6038 Remote Similarity NPC320588
0.6038 Remote Similarity NPC85813
0.6038 Remote Similarity NPC290563
0.6038 Remote Similarity NPC261831
0.6038 Remote Similarity NPC88966
0.6038 Remote Similarity NPC281972
0.6038 Remote Similarity NPC32467
0.6 Remote Similarity NPC476469
0.5965 Remote Similarity NPC235242
0.5962 Remote Similarity NPC303765
0.5952 Remote Similarity NPC223374
0.5952 Remote Similarity NPC301398
0.5952 Remote Similarity NPC86545
0.5952 Remote Similarity NPC196442
0.5946 Remote Similarity NPC314668
0.5946 Remote Similarity NPC230726
0.5932 Remote Similarity NPC226592
0.5926 Remote Similarity NPC45626
0.5918 Remote Similarity NPC326957
0.5918 Remote Similarity NPC249754
0.5909 Remote Similarity NPC326532
0.5897 Remote Similarity NPC248139
0.5897 Remote Similarity NPC292641
0.5893 Remote Similarity NPC329819
0.5882 Remote Similarity NPC59051
0.5833 Remote Similarity NPC273545
0.5818 Remote Similarity NPC477201
0.5818 Remote Similarity NPC278209
0.5818 Remote Similarity NPC18951
0.58 Remote Similarity NPC216130
0.5769 Remote Similarity NPC48162
0.575 Remote Similarity NPC168982
0.575 Remote Similarity NPC198126
0.575 Remote Similarity NPC320981
0.5745 Remote Similarity NPC144829
0.5745 Remote Similarity NPC310220

  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 NPC73245 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
0.8205 Intermediate Similarity NPD9448 Phase 2
0.8205 Intermediate Similarity NPD633 Phase 3
0.8 Intermediate Similarity NPD9635 Discontinued
0.7805 Intermediate Similarity NPD2270 Approved
0.775 Intermediate Similarity NPD9655 Approved
0.7317 Intermediate Similarity NPD9450 Approved
0.7317 Intermediate Similarity NPD77 Approved
0.7273 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD634 Phase 3
0.7073 Intermediate Similarity NPD3206 Approved
0.6923 Remote Similarity NPD8857 Approved
0.6829 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6809 Remote Similarity NPD2266 Phase 2
0.6667 Remote Similarity NPD3173 Approved
0.6458 Remote Similarity NPD622 Approved
0.6444 Remote Similarity NPD387 Clinical (unspecified phase)
0.6383 Remote Similarity NPD9431 Approved
0.6383 Remote Similarity NPD9430 Approved
0.6341 Remote Similarity NPD9447 Approved
0.6304 Remote Similarity NPD9019 Approved
0.6275 Remote Similarity NPD3186 Phase 1
0.617 Remote Similarity NPD2699 Approved
0.6154 Remote Similarity NPD3172 Approved
0.6078 Remote Similarity NPD9638 Phase 2
0.6042 Remote Similarity NPD4222 Approved
0.6042 Remote Similarity NPD3174 Discontinued
0.6038 Remote Similarity NPD3730 Approved
0.6038 Remote Similarity NPD3196 Approved
0.6038 Remote Similarity NPD3728 Approved
0.6038 Remote Similarity NPD4266 Approved
0.6038 Remote Similarity NPD3195 Phase 2
0.6038 Remote Similarity NPD3194 Approved
0.6038 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6038 Remote Similarity NPD615 Clinical (unspecified phase)
0.6 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5926 Remote Similarity NPD9454 Approved
0.5909 Remote Similarity NPD9513 Phase 1
0.5897 Remote Similarity NPD62 Approved
0.58 Remote Similarity NPD6125 Clinical (unspecified phase)
0.575 Remote Similarity NPD8590 Approved
0.575 Remote Similarity NPD8618 Approved
0.5714 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8615 Phase 2
0.5714 Remote Similarity NPD8201 Phase 2
0.5714 Remote Similarity NPD39 Approved
0.5686 Remote Similarity NPD9044 Approved
0.5641 Remote Similarity NPD8594 Approved
0.5641 Remote Similarity NPD8593 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