Structure

Physi-Chem Properties

Molecular Weight:  258.16
Volume:  301.713
LogP:  2.477
LogD:  2.378
LogS:  -3.686
# Rotatable Bonds:  7
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.418
Synthetic Accessibility Score:  4.027
Fsp3:  0.412
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.879
MDCK Permeability:  3.175129313603975e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.776
20% Bioavailability (F20%):  0.234
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  98.41449737548828%
Volume Distribution (VD):  0.5
Pgp-substrate:  2.305950403213501%

ADMET: Metabolism

CYP1A2-inhibitor:  0.623
CYP1A2-substrate:  0.179
CYP2C19-inhibitor:  0.96
CYP2C19-substrate:  0.744
CYP2C9-inhibitor:  0.91
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.917
CYP2D6-substrate:  0.933
CYP3A4-inhibitor:  0.928
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  6.585
Half-life (T1/2):  0.237

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.82
Drug-inuced Liver Injury (DILI):  0.97
AMES Toxicity:  0.527
Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.104
Skin Sensitization:  0.944
Carcinogencity:  0.742
Eye Corrosion:  0.876
Eye Irritation:  0.986
Respiratory Toxicity:  0.83

Download Data

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

  Natural Product: NPC328784

Natural Product ID:  NPC328784
Common Name*:   (Cis)-Heptadeca-8,10,12-Triene-4,6-Diyne-1,14-Diol
IUPAC Name:   (8E,10E,12E)-heptadeca-8,10,12-trien-4,6-diyne-1,14-diol
Synonyms:  
Standard InCHIKey:  FQVNSJQTSOVRKZ-YNQQSWPQSA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-2-14-17(19)15-12-10-8-6-4-3-5-7-9-11-13-16-18/h4,6,8,10,12,15,17-19H,2,11,13-14,16H2,1H3/b6-4+,10-8+,15-12+
SMILES:  CCCC(/C=C/C=C/C=C/C#CC#CCCCO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453245
PubChem CID:   5281132
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPO18101 Cicuta virosa Species Apiaceae Eukaryota subterranean part n.a. n.a. PMID[11087575]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18101 Cicuta virosa Species Apiaceae 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
NPT32 Organism Mus musculus Mus musculus LD50 = 38.6 mg kg-1 i.p. PMID[516353]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus IC50 = 2010.0 nM PMID[516353]

☑ 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 NPC328784 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 NPC291437
0.9375 High Similarity NPC59408
0.9375 High Similarity NPC71053
0.92 High Similarity NPC110732
0.898 High Similarity NPC151782
0.8958 High Similarity NPC302310
0.8958 High Similarity NPC153538
0.8776 High Similarity NPC72699
0.8679 High Similarity NPC472445
0.86 High Similarity NPC93639
0.8571 High Similarity NPC85079
0.8571 High Similarity NPC31194
0.8571 High Similarity NPC248884
0.8542 High Similarity NPC180575
0.8542 High Similarity NPC124183
0.8542 High Similarity NPC35141
0.8478 Intermediate Similarity NPC206906
0.8462 Intermediate Similarity NPC256209
0.8462 Intermediate Similarity NPC49059
0.8333 Intermediate Similarity NPC276825
0.8269 Intermediate Similarity NPC34577
0.82 Intermediate Similarity NPC471280
0.82 Intermediate Similarity NPC125122
0.82 Intermediate Similarity NPC471275
0.82 Intermediate Similarity NPC471276
0.8163 Intermediate Similarity NPC55063
0.8163 Intermediate Similarity NPC19834
0.8125 Intermediate Similarity NPC101616
0.8113 Intermediate Similarity NPC473532
0.8085 Intermediate Similarity NPC304151
0.8077 Intermediate Similarity NPC142092
0.8039 Intermediate Similarity NPC474642
0.8039 Intermediate Similarity NPC473913
0.8039 Intermediate Similarity NPC249670
0.8039 Intermediate Similarity NPC199286
0.8039 Intermediate Similarity NPC477727
0.8039 Intermediate Similarity NPC471281
0.8 Intermediate Similarity NPC44542
0.7963 Intermediate Similarity NPC473896
0.7963 Intermediate Similarity NPC473735
0.7963 Intermediate Similarity NPC473725
0.7963 Intermediate Similarity NPC473721
0.7963 Intermediate Similarity NPC477725
0.7963 Intermediate Similarity NPC473910
0.7963 Intermediate Similarity NPC475353
0.7963 Intermediate Similarity NPC477726
0.7959 Intermediate Similarity NPC269074
0.7925 Intermediate Similarity NPC61177
0.7925 Intermediate Similarity NPC284224
0.7885 Intermediate Similarity NPC129263
0.7885 Intermediate Similarity NPC170776
0.7885 Intermediate Similarity NPC224148
0.7885 Intermediate Similarity NPC55383
0.7885 Intermediate Similarity NPC256656
0.7885 Intermediate Similarity NPC197272
0.7885 Intermediate Similarity NPC475477
0.7885 Intermediate Similarity NPC76198
0.7885 Intermediate Similarity NPC9273
0.7885 Intermediate Similarity NPC294278
0.7885 Intermediate Similarity NPC165447
0.7885 Intermediate Similarity NPC89824
0.7885 Intermediate Similarity NPC329608
0.7885 Intermediate Similarity NPC471959
0.7885 Intermediate Similarity NPC477723
0.7818 Intermediate Similarity NPC161838
0.7818 Intermediate Similarity NPC475384
0.7818 Intermediate Similarity NPC470966
0.7818 Intermediate Similarity NPC470967
0.7818 Intermediate Similarity NPC477661
0.7818 Intermediate Similarity NPC473847
0.7818 Intermediate Similarity NPC471960
0.7818 Intermediate Similarity NPC470968
0.7818 Intermediate Similarity NPC470969
0.78 Intermediate Similarity NPC157096
0.7778 Intermediate Similarity NPC300121
0.7755 Intermediate Similarity NPC138935
0.7755 Intermediate Similarity NPC108195
0.7719 Intermediate Similarity NPC222852
0.7692 Intermediate Similarity NPC474460
0.7679 Intermediate Similarity NPC193975
0.7679 Intermediate Similarity NPC470970
0.76 Intermediate Similarity NPC140501
0.7551 Intermediate Similarity NPC116934
0.7547 Intermediate Similarity NPC474495
0.7547 Intermediate Similarity NPC473672
0.75 Intermediate Similarity NPC324224
0.75 Intermediate Similarity NPC472808
0.7455 Intermediate Similarity NPC48058
0.7447 Intermediate Similarity NPC15934
0.7447 Intermediate Similarity NPC306850
0.7414 Intermediate Similarity NPC322186
0.7414 Intermediate Similarity NPC322002
0.7407 Intermediate Similarity NPC35756
0.7368 Intermediate Similarity NPC212730
0.7368 Intermediate Similarity NPC265551
0.7358 Intermediate Similarity NPC473768
0.7333 Intermediate Similarity NPC29697
0.7321 Intermediate Similarity NPC470963
0.7321 Intermediate Similarity NPC474644
0.7321 Intermediate Similarity NPC152668
0.7321 Intermediate Similarity NPC474913
0.7321 Intermediate Similarity NPC471239
0.7321 Intermediate Similarity NPC146551
0.7321 Intermediate Similarity NPC329686
0.7321 Intermediate Similarity NPC474513
0.7292 Intermediate Similarity NPC329762
0.7292 Intermediate Similarity NPC27444
0.7292 Intermediate Similarity NPC103236
0.7288 Intermediate Similarity NPC327112
0.7273 Intermediate Similarity NPC474496
0.7273 Intermediate Similarity NPC26102
0.7273 Intermediate Similarity NPC477724
0.7273 Intermediate Similarity NPC187361
0.7255 Intermediate Similarity NPC160628
0.7234 Intermediate Similarity NPC34873
0.7234 Intermediate Similarity NPC40434
0.7193 Intermediate Similarity NPC311648
0.7193 Intermediate Similarity NPC473865
0.7193 Intermediate Similarity NPC470964
0.7193 Intermediate Similarity NPC474643
0.7174 Intermediate Similarity NPC79544
0.717 Intermediate Similarity NPC267110
0.7167 Intermediate Similarity NPC66460
0.7167 Intermediate Similarity NPC271282
0.7167 Intermediate Similarity NPC325929
0.7167 Intermediate Similarity NPC475984
0.7143 Intermediate Similarity NPC269823
0.7119 Intermediate Similarity NPC318306
0.7083 Intermediate Similarity NPC103213
0.7083 Intermediate Similarity NPC255042
0.7083 Intermediate Similarity NPC182840
0.7083 Intermediate Similarity NPC29091
0.7069 Intermediate Similarity NPC594
0.7069 Intermediate Similarity NPC474869
0.7069 Intermediate Similarity NPC48968
0.7049 Intermediate Similarity NPC471023
0.7049 Intermediate Similarity NPC470965
0.7021 Intermediate Similarity NPC174396
0.7018 Intermediate Similarity NPC317899
0.7 Intermediate Similarity NPC471278
0.7 Intermediate Similarity NPC46248
0.7 Intermediate Similarity NPC149668
0.7 Intermediate Similarity NPC213538
0.7 Intermediate Similarity NPC256766
0.7 Intermediate Similarity NPC249801
0.6964 Remote Similarity NPC217188
0.6957 Remote Similarity NPC58957
0.6949 Remote Similarity NPC181872
0.6935 Remote Similarity NPC470320
0.6935 Remote Similarity NPC226592
0.6909 Remote Similarity NPC29234
0.6833 Remote Similarity NPC329249
0.6833 Remote Similarity NPC473652
0.6825 Remote Similarity NPC136164
0.6825 Remote Similarity NPC255863
0.6825 Remote Similarity NPC308844
0.6825 Remote Similarity NPC245947
0.6825 Remote Similarity NPC323045
0.6825 Remote Similarity NPC317881
0.6786 Remote Similarity NPC473705
0.678 Remote Similarity NPC71755
0.6739 Remote Similarity NPC250734
0.6739 Remote Similarity NPC81989
0.6727 Remote Similarity NPC225974
0.6727 Remote Similarity NPC20934
0.6727 Remote Similarity NPC288381
0.6727 Remote Similarity NPC473487
0.6724 Remote Similarity NPC227135
0.6721 Remote Similarity NPC328311
0.6719 Remote Similarity NPC146811
0.6667 Remote Similarity NPC194586
0.6667 Remote Similarity NPC209279
0.6667 Remote Similarity NPC180871
0.6667 Remote Similarity NPC68889
0.6667 Remote Similarity NPC51758
0.6667 Remote Similarity NPC469373
0.6667 Remote Similarity NPC108494
0.6667 Remote Similarity NPC67761
0.6667 Remote Similarity NPC88079
0.6667 Remote Similarity NPC226848
0.6615 Remote Similarity NPC49863
0.6613 Remote Similarity NPC26810
0.6613 Remote Similarity NPC477829
0.6613 Remote Similarity NPC55376
0.6613 Remote Similarity NPC168407
0.6607 Remote Similarity NPC200772
0.6604 Remote Similarity NPC76976
0.6562 Remote Similarity NPC323477
0.6557 Remote Similarity NPC122239
0.6557 Remote Similarity NPC475931
0.6552 Remote Similarity NPC269615
0.6545 Remote Similarity NPC475153
0.6538 Remote Similarity NPC252978
0.6508 Remote Similarity NPC55068
0.65 Remote Similarity NPC474577
0.65 Remote Similarity NPC268185
0.65 Remote Similarity NPC121034
0.6491 Remote Similarity NPC106531
0.6462 Remote Similarity NPC129995
0.6462 Remote Similarity NPC328653

  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 NPC328784 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
0.76 Intermediate Similarity NPD4265 Approved
0.7288 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.6667 Remote Similarity NPD585 Clinical (unspecified phase)
0.6615 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6545 Remote Similarity NPD4220 Pre-registration
0.6508 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6333 Remote Similarity NPD4219 Approved
0.6143 Remote Similarity NPD4732 Discontinued
0.6094 Remote Similarity NPD368 Approved
0.6 Remote Similarity NPD4222 Approved
0.6 Remote Similarity NPD39 Approved
0.5972 Remote Similarity NPD8264 Approved
0.5926 Remote Similarity NPD5326 Phase 3
0.5902 Remote Similarity NPD342 Phase 1
0.5873 Remote Similarity NPD6109 Phase 1
0.5857 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5733 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6898 Phase 1
0.569 Remote Similarity NPD3173 Approved
0.5672 Remote Similarity NPD3197 Phase 1

  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