Structure

Physi-Chem Properties

Molecular Weight:  272.18
Volume:  319.009
LogP:  5.122
LogD:  2.655
LogS:  -4.714
# Rotatable Bonds:  10
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.365
Synthetic Accessibility Score:  3.067
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:  -4.856
MDCK Permeability:  5.318212788552046e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.297
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  101.9411849975586%
Volume Distribution (VD):  0.366
Pgp-substrate:  0.587121844291687%

ADMET: Metabolism

CYP1A2-inhibitor:  0.377
CYP1A2-substrate:  0.201
CYP2C19-inhibitor:  0.902
CYP2C19-substrate:  0.279
CYP2C9-inhibitor:  0.889
CYP2C9-substrate:  0.997
CYP2D6-inhibitor:  0.158
CYP2D6-substrate:  0.885
CYP3A4-inhibitor:  0.765
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  1.73
Half-life (T1/2):  0.707

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.599
Drug-inuced Liver Injury (DILI):  0.956
AMES Toxicity:  0.458
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.963
Carcinogencity:  0.678
Eye Corrosion:  0.976
Eye Irritation:  0.98
Respiratory Toxicity:  0.898

Download Data

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

  Natural Product: NPC54766

Natural Product ID:  NPC54766
Common Name*:   13(E),17-Octadecadiene-9,11-Diynoic Acid
IUPAC Name:   (13E)-octadeca-13,17-dien-9,11-diynoic acid
Synonyms:   13,14-dihydrooropheic acid
Standard InCHIKey:  GYLJVPBWGZUNMB-AATRIKPKSA-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/h2,5-6H,1,3-4,11-17H2,(H,19,20)/b6-5+
SMILES:  C=CCC/C=C/C#CC#CCCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL449730
PubChem CID:   10355900
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
NPO431 Mitrephora celebica Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11678665]
NPO40197 Meiogyne baillonii Species Annonaceae Eukaryota Bark n.a. n.a. PMID[29969260]
NPO431 Mitrephora celebica Species Annonaceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 25.0 ug.mL-1 PMID[522398]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 12.5 ug.mL-1 PMID[522398]
NPT25930 SINGLE PROTEIN Rho guanine nucleotide exchange factor 1 Homo sapiens Inhibition = 0.0 % PMID[522399]

☑ 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 NPC54766 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
0.9808 High Similarity NPC179764
0.9808 High Similarity NPC187777
0.9615 High Similarity NPC274290
0.9615 High Similarity NPC473863
0.9412 High Similarity NPC18357
0.9259 High Similarity NPC225929
0.9231 High Similarity NPC294548
0.9231 High Similarity NPC1813
0.9231 High Similarity NPC36061
0.9231 High Similarity NPC139029
0.9091 High Similarity NPC267817
0.9057 High Similarity NPC32467
0.9057 High Similarity NPC85813
0.9057 High Similarity NPC281972
0.9057 High Similarity NPC154245
0.9057 High Similarity NPC290563
0.9057 High Similarity NPC424
0.9057 High Similarity NPC6095
0.9057 High Similarity NPC87564
0.9057 High Similarity NPC88966
0.9057 High Similarity NPC25417
0.9057 High Similarity NPC261831
0.9038 High Similarity NPC281245
0.8868 High Similarity NPC70387
0.8868 High Similarity NPC321062
0.8846 High Similarity NPC470412
0.8846 High Similarity NPC28205
0.8846 High Similarity NPC284212
0.8846 High Similarity NPC470410
0.8772 High Similarity NPC235242
0.8727 High Similarity NPC18951
0.8727 High Similarity NPC477201
0.8679 High Similarity NPC92114
0.8654 High Similarity NPC224227
0.8627 High Similarity NPC207292
0.8627 High Similarity NPC180534
0.8545 High Similarity NPC45626
0.8491 Intermediate Similarity NPC262968
0.8462 Intermediate Similarity NPC5413
0.8462 Intermediate Similarity NPC149821
0.8333 Intermediate Similarity NPC470320
0.8333 Intermediate Similarity NPC129458
0.8333 Intermediate Similarity NPC161366
0.8333 Intermediate Similarity NPC226592
0.8302 Intermediate Similarity NPC59051
0.8276 Intermediate Similarity NPC274927
0.8276 Intermediate Similarity NPC106851
0.8182 Intermediate Similarity NPC71761
0.8182 Intermediate Similarity NPC225066
0.8182 Intermediate Similarity NPC309606
0.8182 Intermediate Similarity NPC39633
0.8182 Intermediate Similarity NPC139545
0.8182 Intermediate Similarity NPC10081
0.8136 Intermediate Similarity NPC251042
0.8136 Intermediate Similarity NPC122521
0.8136 Intermediate Similarity NPC243532
0.8136 Intermediate Similarity NPC174447
0.8103 Intermediate Similarity NPC329819
0.8103 Intermediate Similarity NPC34416
0.8077 Intermediate Similarity NPC42304
0.8 Intermediate Similarity NPC201939
0.8 Intermediate Similarity NPC303765
0.8 Intermediate Similarity NPC174560
0.8 Intermediate Similarity NPC125312
0.8 Intermediate Similarity NPC477829
0.8 Intermediate Similarity NPC40082
0.7925 Intermediate Similarity NPC91495
0.7895 Intermediate Similarity NPC200845
0.7895 Intermediate Similarity NPC10316
0.7895 Intermediate Similarity NPC228473
0.7895 Intermediate Similarity NPC128061
0.7895 Intermediate Similarity NPC28779
0.7895 Intermediate Similarity NPC223677
0.7885 Intermediate Similarity NPC117572
0.7742 Intermediate Similarity NPC68343
0.7742 Intermediate Similarity NPC328089
0.7719 Intermediate Similarity NPC87394
0.7619 Intermediate Similarity NPC136164
0.7619 Intermediate Similarity NPC318420
0.7619 Intermediate Similarity NPC326268
0.7619 Intermediate Similarity NPC245947
0.7619 Intermediate Similarity NPC255863
0.7593 Intermediate Similarity NPC216130
0.7586 Intermediate Similarity NPC52264
0.7586 Intermediate Similarity NPC474672
0.7586 Intermediate Similarity NPC477984
0.75 Intermediate Similarity NPC255837
0.75 Intermediate Similarity NPC19305
0.75 Intermediate Similarity NPC48162
0.75 Intermediate Similarity NPC469373
0.7458 Intermediate Similarity NPC325977
0.7419 Intermediate Similarity NPC321838
0.7419 Intermediate Similarity NPC320305
0.7419 Intermediate Similarity NPC328776
0.7419 Intermediate Similarity NPC475984
0.7414 Intermediate Similarity NPC137538
0.7385 Intermediate Similarity NPC271921
0.7385 Intermediate Similarity NPC330426
0.7385 Intermediate Similarity NPC104537
0.7385 Intermediate Similarity NPC99619
0.7385 Intermediate Similarity NPC127091
0.7385 Intermediate Similarity NPC148192
0.7385 Intermediate Similarity NPC22101
0.7385 Intermediate Similarity NPC26500
0.7358 Intermediate Similarity NPC8219
0.7302 Intermediate Similarity NPC470965
0.7302 Intermediate Similarity NPC29697
0.7273 Intermediate Similarity NPC324981
0.7273 Intermediate Similarity NPC48218
0.7273 Intermediate Similarity NPC476614
0.7273 Intermediate Similarity NPC141481
0.7273 Intermediate Similarity NPC473559
0.7258 Intermediate Similarity NPC143857
0.7258 Intermediate Similarity NPC229252
0.7193 Intermediate Similarity NPC129263
0.7193 Intermediate Similarity NPC470411
0.7188 Intermediate Similarity NPC234767
0.717 Intermediate Similarity NPC270796
0.7164 Intermediate Similarity NPC317583
0.7164 Intermediate Similarity NPC143396
0.7143 Intermediate Similarity NPC207815
0.7143 Intermediate Similarity NPC271282
0.7143 Intermediate Similarity NPC66460
0.7143 Intermediate Similarity NPC325929
0.7121 Intermediate Similarity NPC60120
0.7121 Intermediate Similarity NPC475443
0.7121 Intermediate Similarity NPC473829
0.7119 Intermediate Similarity NPC322461
0.7115 Intermediate Similarity NPC103286
0.7115 Intermediate Similarity NPC163746
0.7097 Intermediate Similarity NPC329550
0.7083 Intermediate Similarity NPC469495
0.7059 Intermediate Similarity NPC476660
0.7059 Intermediate Similarity NPC42526
0.7031 Intermediate Similarity NPC54925
0.7031 Intermediate Similarity NPC477707
0.7018 Intermediate Similarity NPC474391
0.7015 Intermediate Similarity NPC53302
0.6986 Remote Similarity NPC209995
0.6984 Remote Similarity NPC328311
0.6984 Remote Similarity NPC327112
0.6981 Remote Similarity NPC71317
0.6981 Remote Similarity NPC129972
0.6981 Remote Similarity NPC301528
0.697 Remote Similarity NPC142423
0.697 Remote Similarity NPC308294
0.6949 Remote Similarity NPC34577
0.6949 Remote Similarity NPC187361
0.6949 Remote Similarity NPC284224
0.6949 Remote Similarity NPC26102
0.6949 Remote Similarity NPC477724
0.6912 Remote Similarity NPC473772
0.6897 Remote Similarity NPC477458
0.6892 Remote Similarity NPC200446
0.6885 Remote Similarity NPC327388
0.6842 Remote Similarity NPC304162
0.6842 Remote Similarity NPC163345
0.6833 Remote Similarity NPC49059
0.6833 Remote Similarity NPC256209
0.6825 Remote Similarity NPC474267
0.6825 Remote Similarity NPC473652
0.6792 Remote Similarity NPC171736
0.6792 Remote Similarity NPC149184
0.6792 Remote Similarity NPC307783
0.6792 Remote Similarity NPC216630
0.6792 Remote Similarity NPC209970
0.6792 Remote Similarity NPC196924
0.6774 Remote Similarity NPC281230
0.6774 Remote Similarity NPC323597
0.6774 Remote Similarity NPC323436
0.6774 Remote Similarity NPC323498
0.6774 Remote Similarity NPC211752
0.6769 Remote Similarity NPC477830
0.6761 Remote Similarity NPC55527
0.6761 Remote Similarity NPC227396
0.6761 Remote Similarity NPC476046
0.6761 Remote Similarity NPC103958
0.6761 Remote Similarity NPC283908
0.6761 Remote Similarity NPC3753
0.6761 Remote Similarity NPC237591
0.6761 Remote Similarity NPC241854
0.6761 Remote Similarity NPC183503
0.6761 Remote Similarity NPC251970
0.6761 Remote Similarity NPC474321
0.6761 Remote Similarity NPC161923
0.6731 Remote Similarity NPC261080
0.6731 Remote Similarity NPC301585
0.6731 Remote Similarity NPC301696
0.6731 Remote Similarity NPC118968
0.6731 Remote Similarity NPC201844
0.6731 Remote Similarity NPC294085
0.6731 Remote Similarity NPC113928
0.6731 Remote Similarity NPC214610
0.6731 Remote Similarity NPC154186
0.6731 Remote Similarity NPC183424
0.6731 Remote Similarity NPC279026
0.6731 Remote Similarity NPC14227
0.6727 Remote Similarity NPC108195
0.6721 Remote Similarity NPC474513
0.6721 Remote Similarity NPC146551

  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 NPC54766 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
0.9231 High Similarity NPD3172 Approved
0.9057 High Similarity NPD3194 Approved
0.9057 High Similarity NPD4266 Approved
0.9057 High Similarity NPD3196 Approved
0.9057 High Similarity NPD3195 Phase 2
0.8627 High Similarity NPD622 Approved
0.8491 Intermediate Similarity NPD28 Approved
0.8491 Intermediate Similarity NPD29 Approved
0.8462 Intermediate Similarity NPD3173 Approved
0.7885 Intermediate Similarity NPD3174 Discontinued
0.7885 Intermediate Similarity NPD4222 Approved
0.7742 Intermediate Similarity NPD3197 Phase 1
0.7547 Intermediate Similarity NPD39 Approved
0.717 Intermediate Similarity NPD5326 Phase 3
0.6984 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6792 Remote Similarity NPD2270 Approved
0.6731 Remote Similarity NPD9448 Phase 2
0.6731 Remote Similarity NPD9655 Approved
0.6731 Remote Similarity NPD633 Phase 3
0.6667 Remote Similarity NPD5343 Approved
0.6515 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6471 Remote Similarity NPD7331 Phase 2
0.6429 Remote Similarity NPD3199 Clinical (unspecified phase)
0.64 Remote Similarity NPD3732 Approved
0.6377 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6267 Remote Similarity NPD4756 Discovery
0.6234 Remote Similarity NPD5368 Approved
0.6226 Remote Similarity NPD3206 Approved
0.6203 Remote Similarity NPD5332 Approved
0.6203 Remote Similarity NPD5331 Approved
0.619 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6184 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6109 Phase 1
0.6154 Remote Similarity NPD5369 Approved
0.614 Remote Similarity NPD6097 Approved
0.614 Remote Similarity NPD6096 Approved
0.6076 Remote Similarity NPD4270 Approved
0.6076 Remote Similarity NPD6435 Approved
0.6076 Remote Similarity NPD4269 Approved
0.6034 Remote Similarity NPD634 Phase 3
0.6026 Remote Similarity NPD4252 Approved
0.6 Remote Similarity NPD7154 Phase 3
0.6 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6 Remote Similarity NPD5362 Discontinued
0.6 Remote Similarity NPD8039 Approved
0.5974 Remote Similarity NPD4268 Approved
0.5974 Remote Similarity NPD4271 Approved
0.5857 Remote Similarity NPD7341 Phase 2
0.5854 Remote Similarity NPD5363 Approved
0.5823 Remote Similarity NPD4819 Approved
0.5823 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5823 Remote Similarity NPD4820 Approved
0.5823 Remote Similarity NPD4822 Approved
0.5823 Remote Similarity NPD4821 Approved
0.5783 Remote Similarity NPD4623 Approved
0.5783 Remote Similarity NPD5786 Approved
0.5783 Remote Similarity NPD4519 Discontinued
0.5775 Remote Similarity NPD3704 Approved
0.5763 Remote Similarity NPD9430 Approved
0.5763 Remote Similarity NPD9431 Approved
0.575 Remote Similarity NPD857 Phase 3
0.575 Remote Similarity NPD226 Approved
0.575 Remote Similarity NPD4790 Discontinued
0.5738 Remote Similarity NPD4220 Pre-registration
0.5714 Remote Similarity NPD4793 Discontinued
0.5714 Remote Similarity NPD3186 Phase 1
0.5663 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5647 Remote Similarity NPD4518 Approved
0.561 Remote Similarity NPD9491 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