Structure

Physi-Chem Properties

Molecular Weight:  272.18
Volume:  319.009
LogP:  5.718
LogD:  2.759
LogS:  -5.384
# Rotatable Bonds:  9
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.509
Synthetic Accessibility Score:  2.842
Fsp3:  0.611
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:  -4.894
MDCK Permeability:  4.8520312702748924e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.142
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  102.6039810180664%
Volume Distribution (VD):  0.631
Pgp-substrate:  0.917731523513794%

ADMET: Metabolism

CYP1A2-inhibitor:  0.637
CYP1A2-substrate:  0.184
CYP2C19-inhibitor:  0.81
CYP2C19-substrate:  0.425
CYP2C9-inhibitor:  0.755
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.353
CYP3A4-inhibitor:  0.338
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  2.782
Half-life (T1/2):  0.62

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.155
Drug-inuced Liver Injury (DILI):  0.979
AMES Toxicity:  0.519
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.962
Carcinogencity:  0.34
Eye Corrosion:  0.987
Eye Irritation:  0.97
Respiratory Toxicity:  0.728

Download Data

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

  Natural Product: NPC255837

Natural Product ID:  NPC255837
Common Name*:   Octadeca-8,10,12-Triynoic Acid
IUPAC Name:   octadeca-8,10,12-triynoic acid
Synonyms:  
Standard InCHIKey:  ZRDMQHHJJMWDNV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H24O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-5,12-17H2,1H3,(H,19,20)/p-1
SMILES:  CCCCCC#CC#CC#CCCCCCCC(=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464527
PubChem CID:   10468473
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
NPO27826 Sinularia maxima Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[23200246]
NPO32503 heisteria acuminata Species Erythropalaceae Eukaryota bark n.a. n.a. PMID[9584394]
NPO27754 Rubia oncotricha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27754 Rubia oncotricha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18828 Iryanthera coriacea Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28329 Cereus candicans Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28212 Ilex purpurea Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27754 Rubia oncotricha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28173 Boronia coerulescens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27826 Sinularia maxima Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3112 Honorius nutans Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28387 Acanthophyllum elatius Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28104 Streptomyces hachijoensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28155 Perezia carpholepis Species Pereziidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14372 Melochia tomentosa Species Malvaceae 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
NPT2 Others Unspecified Inhibition = 45.0 % PMID[530428]
NPT2 Others Unspecified Inhibition = 33.0 % PMID[530428]
NPT2 Others Unspecified Inhibition = 21.0 % PMID[530428]

☑ 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 NPC255837 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 NPC19305
0.9756 High Similarity NPC8219
0.95 High Similarity NPC103286
0.95 High Similarity NPC163746
0.9268 High Similarity NPC71317
0.9268 High Similarity NPC129972
0.9268 High Similarity NPC301528
0.9024 High Similarity NPC149184
0.9024 High Similarity NPC216630
0.9024 High Similarity NPC171736
0.9024 High Similarity NPC209970
0.9024 High Similarity NPC307783
0.9024 High Similarity NPC196924
0.9 High Similarity NPC301585
0.9 High Similarity NPC301696
0.9 High Similarity NPC201844
0.9 High Similarity NPC14227
0.9 High Similarity NPC261080
0.9 High Similarity NPC113928
0.9 High Similarity NPC279026
0.9 High Similarity NPC154186
0.8889 High Similarity NPC304162
0.881 High Similarity NPC67462
0.875 High Similarity NPC73245
0.8605 High Similarity NPC74845
0.8537 High Similarity NPC118968
0.8537 High Similarity NPC214610
0.8537 High Similarity NPC294085
0.8537 High Similarity NPC183424
0.8511 High Similarity NPC470410
0.8511 High Similarity NPC470412
0.85 High Similarity NPC158179
0.8293 Intermediate Similarity NPC268826
0.825 Intermediate Similarity NPC155263
0.8222 Intermediate Similarity NPC12438
0.8222 Intermediate Similarity NPC30195
0.8125 Intermediate Similarity NPC100096
0.8043 Intermediate Similarity NPC21844
0.8043 Intermediate Similarity NPC324004
0.8043 Intermediate Similarity NPC328497
0.8 Intermediate Similarity NPC156630
0.8 Intermediate Similarity NPC55023
0.7959 Intermediate Similarity NPC18357
0.7907 Intermediate Similarity NPC12156
0.7907 Intermediate Similarity NPC161097
0.7907 Intermediate Similarity NPC28598
0.7872 Intermediate Similarity NPC324793
0.7872 Intermediate Similarity NPC106872
0.7872 Intermediate Similarity NPC477878
0.7857 Intermediate Similarity NPC54980
0.7857 Intermediate Similarity NPC22903
0.7857 Intermediate Similarity NPC201622
0.7857 Intermediate Similarity NPC305660
0.7826 Intermediate Similarity NPC314679
0.7805 Intermediate Similarity NPC134782
0.7692 Intermediate Similarity NPC179764
0.7692 Intermediate Similarity NPC187777
0.7674 Intermediate Similarity NPC219536
0.7674 Intermediate Similarity NPC31551
0.7556 Intermediate Similarity NPC236579
0.7556 Intermediate Similarity NPC203531
0.7551 Intermediate Similarity NPC90904
0.75 Intermediate Similarity NPC473863
0.75 Intermediate Similarity NPC175342
0.75 Intermediate Similarity NPC250028
0.75 Intermediate Similarity NPC40597
0.75 Intermediate Similarity NPC149299
0.75 Intermediate Similarity NPC131770
0.75 Intermediate Similarity NPC54766
0.75 Intermediate Similarity NPC256163
0.75 Intermediate Similarity NPC165533
0.75 Intermediate Similarity NPC200618
0.75 Intermediate Similarity NPC274290
0.7391 Intermediate Similarity NPC317128
0.7347 Intermediate Similarity NPC26253
0.7333 Intermediate Similarity NPC248763
0.7333 Intermediate Similarity NPC53541
0.7333 Intermediate Similarity NPC325452
0.7273 Intermediate Similarity NPC80234
0.7273 Intermediate Similarity NPC223249
0.7255 Intermediate Similarity NPC161366
0.7234 Intermediate Similarity NPC287231
0.7234 Intermediate Similarity NPC469781
0.7234 Intermediate Similarity NPC47363
0.7222 Intermediate Similarity NPC225929
0.7174 Intermediate Similarity NPC289686
0.7143 Intermediate Similarity NPC180534
0.7115 Intermediate Similarity NPC139029
0.7115 Intermediate Similarity NPC36061
0.7115 Intermediate Similarity NPC294548
0.7115 Intermediate Similarity NPC72722
0.7115 Intermediate Similarity NPC1813
0.7083 Intermediate Similarity NPC166287
0.7073 Intermediate Similarity NPC18224
0.7073 Intermediate Similarity NPC328710
0.7059 Intermediate Similarity NPC284212
0.7021 Intermediate Similarity NPC76051
0.6981 Remote Similarity NPC424
0.6981 Remote Similarity NPC85813
0.6981 Remote Similarity NPC154245
0.6981 Remote Similarity NPC469937
0.6981 Remote Similarity NPC32467
0.6981 Remote Similarity NPC25417
0.6981 Remote Similarity NPC23155
0.6981 Remote Similarity NPC290563
0.6981 Remote Similarity NPC88966
0.6981 Remote Similarity NPC320588
0.6981 Remote Similarity NPC87564
0.6981 Remote Similarity NPC87394
0.6981 Remote Similarity NPC6095
0.6981 Remote Similarity NPC261831
0.6981 Remote Similarity NPC53463
0.6981 Remote Similarity NPC281972
0.6923 Remote Similarity NPC281245
0.6889 Remote Similarity NPC3531
0.6863 Remote Similarity NPC50457
0.6842 Remote Similarity NPC235242
0.6818 Remote Similarity NPC252843
0.6818 Remote Similarity NPC109026
0.6792 Remote Similarity NPC321062
0.6792 Remote Similarity NPC70387
0.6786 Remote Similarity NPC267817
0.678 Remote Similarity NPC226592
0.675 Remote Similarity NPC174368
0.6744 Remote Similarity NPC317203
0.6735 Remote Similarity NPC63182
0.6735 Remote Similarity NPC145045
0.6735 Remote Similarity NPC52700
0.6735 Remote Similarity NPC105329
0.6731 Remote Similarity NPC470411
0.6731 Remote Similarity NPC28205
0.6727 Remote Similarity NPC477201
0.6727 Remote Similarity NPC18951
0.6667 Remote Similarity NPC326532
0.6604 Remote Similarity NPC92114
0.66 Remote Similarity NPC326957
0.6591 Remote Similarity NPC80641
0.6591 Remote Similarity NPC154642
0.6591 Remote Similarity NPC80396
0.6538 Remote Similarity NPC55678
0.6538 Remote Similarity NPC224227
0.6531 Remote Similarity NPC273545
0.6512 Remote Similarity NPC57499
0.65 Remote Similarity NPC470320
0.6471 Remote Similarity NPC216130
0.6444 Remote Similarity NPC128996
0.6415 Remote Similarity NPC287811
0.6415 Remote Similarity NPC262968
0.6379 Remote Similarity NPC274927
0.6379 Remote Similarity NPC469924
0.6379 Remote Similarity NPC470363
0.6379 Remote Similarity NPC106851
0.6364 Remote Similarity NPC301398
0.6364 Remote Similarity NPC223374
0.6364 Remote Similarity NPC196442
0.6364 Remote Similarity NPC289979
0.6364 Remote Similarity NPC86545
0.6349 Remote Similarity NPC82315
0.6346 Remote Similarity NPC476469
0.6346 Remote Similarity NPC149821
0.6346 Remote Similarity NPC5413
0.6296 Remote Similarity NPC310746
0.6275 Remote Similarity NPC249754
0.6275 Remote Similarity NPC42304
0.6271 Remote Similarity NPC251042
0.6271 Remote Similarity NPC122521
0.6271 Remote Similarity NPC469921
0.6271 Remote Similarity NPC174447
0.6271 Remote Similarity NPC243532
0.625 Remote Similarity NPC45626
0.625 Remote Similarity NPC474361
0.6226 Remote Similarity NPC59051
0.6226 Remote Similarity NPC305182
0.6207 Remote Similarity NPC329819
0.619 Remote Similarity NPC168982
0.6182 Remote Similarity NPC139545
0.6182 Remote Similarity NPC39633
0.6182 Remote Similarity NPC309606
0.617 Remote Similarity NPC471282
0.617 Remote Similarity NPC81263
0.6167 Remote Similarity NPC469923
0.6167 Remote Similarity NPC201939
0.6167 Remote Similarity NPC40082
0.6154 Remote Similarity NPC207292
0.6136 Remote Similarity NPC7814
0.6136 Remote Similarity NPC127142
0.6136 Remote Similarity NPC154396
0.6136 Remote Similarity NPC286498
0.6122 Remote Similarity NPC176500
0.6111 Remote Similarity NPC314084
0.6102 Remote Similarity NPC17935
0.6102 Remote Similarity NPC475821
0.6087 Remote Similarity NPC74352
0.6078 Remote Similarity NPC308301
0.6066 Remote Similarity NPC235788
0.6066 Remote Similarity NPC474552
0.6047 Remote Similarity NPC76608
0.6047 Remote Similarity NPC16578
0.6047 Remote Similarity NPC225318
0.6047 Remote Similarity NPC149101

  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 NPC255837 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
0.9024 High Similarity NPD2270 Approved
0.9 High Similarity NPD9448 Phase 2
0.9 High Similarity NPD633 Phase 3
0.8537 High Similarity NPD9655 Approved
0.8409 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.8293 Intermediate Similarity NPD3206 Approved
0.7826 Intermediate Similarity NPD634 Phase 3
0.7255 Intermediate Similarity NPD3186 Phase 1
0.7234 Intermediate Similarity NPD2699 Approved
0.7174 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD622 Approved
0.7115 Intermediate Similarity NPD3172 Approved
0.7111 Intermediate Similarity NPD9635 Discontinued
0.7083 Intermediate Similarity NPD9430 Approved
0.7083 Intermediate Similarity NPD9431 Approved
0.6981 Remote Similarity NPD3195 Phase 2
0.6981 Remote Similarity NPD3730 Approved
0.6981 Remote Similarity NPD3196 Approved
0.6981 Remote Similarity NPD4266 Approved
0.6981 Remote Similarity NPD3728 Approved
0.6981 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6981 Remote Similarity NPD3194 Approved
0.6889 Remote Similarity NPD77 Approved
0.6889 Remote Similarity NPD9450 Approved
0.6667 Remote Similarity NPD615 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9513 Phase 1
0.6471 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6471 Remote Similarity NPD2266 Phase 2
0.6444 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6415 Remote Similarity NPD29 Approved
0.6415 Remote Similarity NPD9638 Phase 2
0.6415 Remote Similarity NPD28 Approved
0.6379 Remote Similarity NPD3198 Approved
0.6346 Remote Similarity NPD3173 Approved
0.6136 Remote Similarity NPD8857 Approved
0.6 Remote Similarity NPD9447 Approved
0.5968 Remote Similarity NPD3197 Phase 1
0.5968 Remote Similarity NPD7909 Approved
0.5909 Remote Similarity NPD5383 Approved
0.5909 Remote Similarity NPD2272 Approved
0.5902 Remote Similarity NPD9676 Phase 3
0.5781 Remote Similarity NPD4224 Phase 2
0.5769 Remote Similarity NPD4222 Approved
0.5769 Remote Similarity NPD3174 Discontinued
0.5738 Remote Similarity NPD9656 Approved
0.5686 Remote Similarity NPD9019 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