Structure

Physi-Chem Properties

Molecular Weight:  302.3
Volume:  378.522
LogP:  7.959
LogD:  4.698
LogS:  -3.986
# Rotatable Bonds:  16
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.156
Synthetic Accessibility Score:  2.592
Fsp3:  0.727
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.894
MDCK Permeability:  1.9639821402961388e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.056
20% Bioavailability (F20%):  0.956
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.009
Plasma Protein Binding (PPB):  99.62498474121094%
Volume Distribution (VD):  4.001
Pgp-substrate:  0.5685805082321167%

ADMET: Metabolism

CYP1A2-inhibitor:  0.191
CYP1A2-substrate:  0.2
CYP2C19-inhibitor:  0.477
CYP2C19-substrate:  0.098
CYP2C9-inhibitor:  0.161
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.551
CYP2D6-substrate:  0.915
CYP3A4-inhibitor:  0.562
CYP3A4-substrate:  0.094

ADMET: Excretion

Clearance (CL):  3.442
Half-life (T1/2):  0.293

ADMET: Toxicity

hERG Blockers:  0.418
Human Hepatotoxicity (H-HT):  0.2
Drug-inuced Liver Injury (DILI):  0.861
AMES Toxicity:  0.137
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.063
Skin Sensitization:  0.973
Carcinogencity:  0.139
Eye Corrosion:  0.976
Eye Irritation:  0.985
Respiratory Toxicity:  0.895

Download Data

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

  Natural Product: NPC182392

Natural Product ID:  NPC182392
Common Name*:   Docosa-(3E,15Z)-Dien-1-Yne
IUPAC Name:   (3E,15Z)-docosa-3,15-dien-1-yne
Synonyms:  
Standard InCHIKey:  JJKRBORDDAKFCT-TZXBVGHOSA-N
Standard InCHI:  InChI=1S/C22H38/c1-3-5-7-9-11-13-15-17-19-21-22-20-18-16-14-12-10-8-6-4-2/h1,5,7,14,16H,4,6,8-13,15,17-22H2,2H3/b7-5+,16-14-
SMILES:  C#C/C=C/CCCCCCCCCC/C=CCCCCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL500758
PubChem CID:   44584674
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0001566] Enynes

*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
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. Caribbean n.a. PMID[1431945]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8691203]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8984159]
NPO15047 Cribrochalina vasculum Species Niphatidae 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
NPT176 Organism Artemia salina Artemia salina LC50 = 1.1 ug.mL-1 PMID[534141]

☑ 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 NPC182392 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 NPC62779
0.9062 High Similarity NPC151719
0.8485 Intermediate Similarity NPC196831
0.8438 Intermediate Similarity NPC34671
0.8125 Intermediate Similarity NPC179103
0.8125 Intermediate Similarity NPC76765
0.8125 Intermediate Similarity NPC138325
0.7941 Intermediate Similarity NPC471327
0.75 Intermediate Similarity NPC266539
0.75 Intermediate Similarity NPC266144
0.75 Intermediate Similarity NPC31891
0.75 Intermediate Similarity NPC287191
0.7353 Intermediate Similarity NPC115959
0.7353 Intermediate Similarity NPC123965
0.7317 Intermediate Similarity NPC149668
0.7188 Intermediate Similarity NPC88325
0.7188 Intermediate Similarity NPC38513
0.7105 Intermediate Similarity NPC92224
0.7027 Intermediate Similarity NPC99088
0.7027 Intermediate Similarity NPC173592
0.7027 Intermediate Similarity NPC305759
0.6977 Remote Similarity NPC145755
0.6977 Remote Similarity NPC108195
0.6977 Remote Similarity NPC267514
0.6957 Remote Similarity NPC474642
0.6957 Remote Similarity NPC249670
0.6957 Remote Similarity NPC473913
0.6944 Remote Similarity NPC3649
0.6944 Remote Similarity NPC100879
0.6889 Remote Similarity NPC471958
0.6857 Remote Similarity NPC138113
0.6829 Remote Similarity NPC103236
0.6829 Remote Similarity NPC27444
0.6829 Remote Similarity NPC329762
0.6818 Remote Similarity NPC269074
0.675 Remote Similarity NPC266298
0.6667 Remote Similarity NPC55063
0.6667 Remote Similarity NPC19834
0.6667 Remote Similarity NPC60288
0.6596 Remote Similarity NPC477727
0.6596 Remote Similarity NPC199286
0.6596 Remote Similarity NPC471281
0.6486 Remote Similarity NPC206088
0.6486 Remote Similarity NPC66577
0.6458 Remote Similarity NPC55383
0.6458 Remote Similarity NPC76198
0.6458 Remote Similarity NPC89824
0.6458 Remote Similarity NPC329608
0.6458 Remote Similarity NPC477723
0.6458 Remote Similarity NPC475477
0.6458 Remote Similarity NPC294278
0.6458 Remote Similarity NPC471959
0.6458 Remote Similarity NPC197272
0.6458 Remote Similarity NPC9273
0.6458 Remote Similarity NPC165447
0.6458 Remote Similarity NPC224148
0.6458 Remote Similarity NPC256656
0.6458 Remote Similarity NPC170776
0.6444 Remote Similarity NPC276825
0.6444 Remote Similarity NPC76976
0.6383 Remote Similarity NPC471275
0.6383 Remote Similarity NPC31194
0.6383 Remote Similarity NPC85079
0.6383 Remote Similarity NPC248884
0.6383 Remote Similarity NPC471280
0.6383 Remote Similarity NPC125122
0.6383 Remote Similarity NPC471276
0.6341 Remote Similarity NPC229262
0.6341 Remote Similarity NPC297643
0.6341 Remote Similarity NPC139717
0.6304 Remote Similarity NPC110234
0.6304 Remote Similarity NPC180575
0.6304 Remote Similarity NPC323445
0.6304 Remote Similarity NPC44363
0.6304 Remote Similarity NPC163751
0.6279 Remote Similarity NPC270170
0.6279 Remote Similarity NPC7754
0.6275 Remote Similarity NPC474644
0.625 Remote Similarity NPC282119
0.625 Remote Similarity NPC72699
0.6222 Remote Similarity NPC101616
0.6216 Remote Similarity NPC16561
0.62 Remote Similarity NPC477724
0.62 Remote Similarity NPC187361
0.62 Remote Similarity NPC26102
0.619 Remote Similarity NPC217923
0.617 Remote Similarity NPC124851
0.6154 Remote Similarity NPC474643
0.6154 Remote Similarity NPC473865
0.6136 Remote Similarity NPC67920
0.6136 Remote Similarity NPC287397
0.6136 Remote Similarity NPC177470
0.6136 Remote Similarity NPC304151
0.6136 Remote Similarity NPC298710
0.6122 Remote Similarity NPC151782
0.6111 Remote Similarity NPC262789
0.6111 Remote Similarity NPC64176
0.6111 Remote Similarity NPC288991
0.6098 Remote Similarity NPC34764
0.6098 Remote Similarity NPC216416
0.6098 Remote Similarity NPC190810
0.6098 Remote Similarity NPC76145
0.6087 Remote Similarity NPC474202
0.6087 Remote Similarity NPC239754
0.6087 Remote Similarity NPC49088
0.6087 Remote Similarity NPC474362
0.6078 Remote Similarity NPC473532
0.6078 Remote Similarity NPC48058
0.6061 Remote Similarity NPC47161
0.6047 Remote Similarity NPC183670
0.6042 Remote Similarity NPC98284
0.6042 Remote Similarity NPC17810
0.6042 Remote Similarity NPC302310
0.6042 Remote Similarity NPC153538
0.6038 Remote Similarity NPC471277
0.6038 Remote Similarity NPC471279
0.6 Remote Similarity NPC252978
0.5962 Remote Similarity NPC473721
0.5962 Remote Similarity NPC146551
0.5962 Remote Similarity NPC477725
0.5962 Remote Similarity NPC474513
0.5962 Remote Similarity NPC473735
0.5962 Remote Similarity NPC470963
0.5962 Remote Similarity NPC475353
0.5962 Remote Similarity NPC477726
0.5962 Remote Similarity NPC473910
0.5962 Remote Similarity NPC473896
0.5962 Remote Similarity NPC473725
0.5957 Remote Similarity NPC157096
0.5957 Remote Similarity NPC35141
0.5957 Remote Similarity NPC124183
0.5952 Remote Similarity NPC92863
0.5952 Remote Similarity NPC155880
0.5952 Remote Similarity NPC239039
0.5938 Remote Similarity NPC178306
0.5918 Remote Similarity NPC474391
0.5918 Remote Similarity NPC59051
0.5909 Remote Similarity NPC120926
0.5909 Remote Similarity NPC218918
0.5909 Remote Similarity NPC144023
0.5909 Remote Similarity NPC33489
0.5897 Remote Similarity NPC213749
0.5854 Remote Similarity NPC213767
0.5849 Remote Similarity NPC473847
0.5849 Remote Similarity NPC470964
0.5849 Remote Similarity NPC470967
0.5849 Remote Similarity NPC470969
0.5849 Remote Similarity NPC470966
0.5849 Remote Similarity NPC311648
0.5849 Remote Similarity NPC475384
0.5849 Remote Similarity NPC161838
0.5849 Remote Similarity NPC477661
0.5849 Remote Similarity NPC470968
0.5849 Remote Similarity NPC471960
0.5814 Remote Similarity NPC15934
0.58 Remote Similarity NPC262968
0.58 Remote Similarity NPC59408
0.58 Remote Similarity NPC261571
0.58 Remote Similarity NPC477458
0.58 Remote Similarity NPC129263
0.58 Remote Similarity NPC71053
0.58 Remote Similarity NPC93639
0.5778 Remote Similarity NPC473912
0.5778 Remote Similarity NPC206906
0.5769 Remote Similarity NPC269615
0.5769 Remote Similarity NPC49059
0.5769 Remote Similarity NPC256209
0.5741 Remote Similarity NPC48968
0.5741 Remote Similarity NPC470970
0.5741 Remote Similarity NPC594
0.5714 Remote Similarity NPC207815
0.5714 Remote Similarity NPC471278
0.5714 Remote Similarity NPC17518
0.5714 Remote Similarity NPC22765
0.5686 Remote Similarity NPC188341
0.5686 Remote Similarity NPC92114
0.5686 Remote Similarity NPC142092
0.5686 Remote Similarity NPC106531
0.5686 Remote Similarity NPC49494
0.566 Remote Similarity NPC471239
0.566 Remote Similarity NPC152668
0.566 Remote Similarity NPC477984
0.566 Remote Similarity NPC474672
0.5652 Remote Similarity NPC86538
0.5652 Remote Similarity NPC109813
0.5652 Remote Similarity NPC60556
0.5625 Remote Similarity NPC100380
0.5625 Remote Similarity NPC225855
0.56 Remote Similarity NPC182102
0.56 Remote Similarity NPC224227
0.56 Remote Similarity NPC26960

  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 NPC182392 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
0.6098 Remote Similarity NPD319 Phase 1
0.6042 Remote Similarity NPD8262 Approved
0.5814 Remote Similarity NPD5783 Phase 3
0.58 Remote Similarity NPD28 Approved
0.58 Remote Similarity NPD29 Approved
0.5745 Remote Similarity NPD39 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